# awesome-genome-visualization

**Repository Path**: Dledger/awesome-genome-visualization

## Basic Information

- **Project Name**: awesome-genome-visualization
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-03-13
- **Last Updated**: 2024-10-18

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# awesome-genome-visualization

A list of interesting genome visualizers, genome browsers, or
genome-browser-like implementations

See the new companion website here
https://cmdcolin.github.io/awesome-genome-visualization/

Follow the Twitter account here too :) https://twitter.com/awesomegenomev1

Note that the organization on the GitHub README here is a best effort
categorization using the first tag applied to each tool, but tools can have
multiple tags too. See the website to see all tags applied to tools

The general focus here is on tools that plot things in genomic or sequence
coordinate space

Note: This list runs the gammut from bespoke and simple to more general-purpose
and complex tools. Some are historical, or may be for more visual inspiration
only

I also encourage you to make your own visualization, things like R make this so
much easier! But also consider making your visualization code re-usable for the
wider community! And feel free to send PRs for more tools!

## General

- [Genoverse](https://github.com/wtsi-web/Genoverse)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoverse.png)
- [BasePlayer](https://baseplayer.fi/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/baseplayer.png)
- [Celera genome browser](https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/celera.jpeg)
- [IGB](https://bioviz.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igb.jpg)
- [IGV](https://igv.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igv.jpg)
- [Savant](http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/savant.jpg)
- [Tablet](https://ics.hutton.ac.uk/tablet/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tablet.jpeg)
- [Biodalliance](http://www.biodalliance.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance.png)
- [Ensembl genome browser](https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ensembl.png)
- [Ensembl genome browser 2020 edition](http://2020.ensembl.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/2020ensembl.png)
- [GBrowse 2](http://gmod.org/wiki/GBrowse) (Original gbrowse paper
  https://doi.org/10.1101/gr.403602)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse.png)
- [GenomeMaps](http://www.genomemaps.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomemaps.jpg)
- [Gosling](https://gosling.js.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gosling.png)
- [HiGlass](https://higlass.io)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/higlass.png)
- [IGV.js](https://github.com/igvteam/igv.js/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igvjs.png)
- [JBrowse](http://jbrowse.org/jbrowse1.html) (See also JBrowse plugin registry
  https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app
  using Electron)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse.png)
- [JBrowse 2](http://jbrowse.org/jb2) (See gallery for more examples
  https://jbrowse.org/jb2/gallery)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse2.png)
- [Kero-BROWSE](https://kero.hgc.jp/examples/CLCL/hg38/index.html) (Also can
  visualize basic synteny, see tracks e.g.
  https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human
  vs chimp)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/kerobrowse.png)
- [NCBI Genome Data Viewer](https://www.ncbi.nlm.nih.gov/genome/gdv/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gdv.png)
- [Nucleome browser](https://vis.nucleome.org/v1/main.html) (github at
  https://github.com/nucleome)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucleome.png)
- [Pileup.js](https://github.com/hammerlab/pileup.js)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileupjs.png)
- [Trackster](https://galaxyproject.org/learn/visualization/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackster.png)
- [UCSC genome browser](https://genome.ucsc.edu/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc.jpg)
- [Valis browser](https://valis.bio/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/valis.png)
- [WashU epigenomics browser](https://epigenomegateway.wustl.edu/) (The ReactJS
  is a redesign, there is also a legacy version. Note also, there are
  comparative features
  https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/washu.png)
- [Zenbu](http://fantom.gsc.riken.jp/zenbu/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/zenbu.png)
- [UTGB (University of Tokyo Genome Browser)](http://utgenome.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/utgb.png)
- [Argo](https://web.archive.org/web/20070924141423/http://www.broad.mit.edu/annotation/argo/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/argo.png)
- [ABrowse (genome browser)](undefined) (Had integrations with BioMart, Taverna)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse2.png)
- [gtracks](https://gitlab.com/salk-tm/gtracks) (Powered by pyGenomeTracks)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtracks.png)
- [trackplot (python)](https://github.com/ygidtu/trackplot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot_python.png)

## Commercial

- [10x genomics/Loupe](https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/10xgenomics.png)
- [Alamut](https://www.interactive-biosoftware.com/alamut-visual/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alamut.png)
- [ATCC Genome Portal](https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/atcc.png)
- [Benchling](https://www.benchling.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/benchling.png)
- [CLC Genomics workbench](https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clcgenomics.png)
- [DNASTAR](https://www.dnastar.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnastar.png)
- [Geneious](https://www.geneious.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneious.png)
- [Genestack](https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genestack.png)
- [Golden Helix](http://goldenhelix.com/GenomeBrowse/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/goldenhelix.png)
- [Lucid viewer](https://lucidalign.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lucidalign.png)
- [MacVector](https://macvector.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/macvector.png)
- [Persephone](https://persephonesoft.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/persephone.jpg)
- [SnapGene](https://www.snapgene.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snapgene.png)
- [Strand NGS](https://www.strand-ngs.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/strandngs.png)
- [Bionano](https://bionanogenomics.com/technology/structural-variation/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bionano.png)
- [Circa](https://omgenomics.com/circa)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circa.png)
- [ERGO](https://www.igenbio.com/ergo)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ergo.png)

## MSA

- [AA (alignment annotator)](http://www.bioinformatics.org/strap/aa) (also see
  STRAP) [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aa.png)
- [abrowse (MSA viewer)](https://github.com/ihh/abrowse)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse.png)
- [alignment.js](https://github.com/veg/alignment.js)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentjs.png)
- [AlignmentComparator](http://bioinfweb.info/AlignmentComparator/) (Uses
  http://bioinfweb.info/LibrAlign/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentcomparator.png)
- [AlignmentViewer](https://alignmentviewer.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentviewer.png)
- [AliView](http://www.ormbunkar.se/aliview/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aliview.png)
- [BioJS/MSA](https://msa.biojs.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biojsmsa.png)
- [rMSA](https://github.com/mhahsler/rMSA/blob/master/vignettes/rMSA_vignette.pdf)
  (Can automate boxshade)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rmsa.png)
- [Boxshade](https://embnet.vital-it.ch/software/BOX_form.html) (Also available
  as a command line tool with `apt install boxshade`. See also rMSA which can
  automate running boxshade from within R)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/boxshade.png)
- [ESPript](http://espript.ibcp.fr/ESPript/ESPript/) (Primarily a web interface
  but can download a binary for linux
  https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/espript.png)
- [Jalview](https://www.jalview.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jalview.jpg)
- [JSAV](http://www.bioinf.org.uk/software/jsav)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jsav.png)
- [MSABrowser](https://thekaplanlab.github.io/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/msabrowser.png)
- [msaR](https://github.com/zachcp/msaR) (uses BioJS/MSA)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/msar.png)
- [MView](https://www.ebi.ac.uk/Tools/msa/mview/) (See also their web versions
  of clustal omega etc. which have similar outputs)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mview.png)
- [NCBI MSA Viewer](https://www.ncbi.nlm.nih.gov/projects/msaviewer/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbimsa.png)
- [pyBoxshade](https://github.com/mdbaron42/pyBoxshade) (also see boxshade)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pyboxshade.png)
- [pymsaplotter](https://github.com/orangeSi/pymsaploter)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pymsaplotter.png)
- [React MSAViewer](https://github.com/plotly/react-msa-viewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msa-viewer.png)
- [react-msaview](https://github.com/GMOD/react-msaview)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msaview.png)
- [seqotron](https://github.com/4ment/seqotron)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqotron.png)
- [STRAP](http://www.bioinformatics.org/strap/) (also see AA)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/strap.png)
- [TeXShade](http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/texshade.png)
- [Wasabi](http://wasabiapp.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasabi.png)
- [SNIPViz](http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpviz.png)
- [ALVIS (MSA viewer)](https://www.ebi.ac.uk/research/goldman/software/alvis)
  (Introduces sequence bundles concept, also see web app version
  https://www.ebi.ac.uk/goldman-srv/sequencebundles/ source code
  https://bitbucket.org/schwarzlab/alvis/src/master/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis.png)
- [alignfigR](https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignfigr.png)
- [alen](https://github.com/jakobnissen/alen)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alen.png)
- [ProViz](http://slim.icr.ac.uk/proviz/index.php) (See also alphafold
  visualization as tracks
  http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/proviz.png)
- [MEGA-X](https://www.megasoftware.net/) (original paper from 1994 but actively
  updated. requires EULA for download)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/megax.png)
- [AliTreeViz](https://www.npmjs.com/package/alitreeviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitreeviz.png)
- [ete](http://etetoolkit.org/gallery/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ete.png)
- [ggtree](https://github.com/YuLab-SMU/ggtree) (see
  https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA
  example)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtree.png)
- [seqvisr](https://github.com/vragh/seqvisr/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqvisr.png)
- [Seaview](http://doua.prabi.fr/software/seaview)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seaview.png)
- [CIAlign](undefined) (Has useful utility functions to clean gaps and trim
  MSAs)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cialign.png)
- [ggmsa](http://yulab-smu.top/ggmsa/) (See also ggtree)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggmsa.png)
- [CView](https://sourceforge.net/projects/cview/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cview.png)

## Logo

- [LogoJS](https://logojs.wenglab.org/app/gallery/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/logojs.png)

## CNV

- [aCNVViewer](https://github.com/FJD-CEPH/aCNViewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/acnvviewer.png)
- [CNVkit](https://cnvkit.readthedocs.io/en/stable/plots.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvkit.png)
- [BAMScale](https://github.com/ncbi/BAMscale)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscale.png)
- [cnvCurator](http://www.acsu.buffalo.edu/~lm69/cnvCurator)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvcurator.png)
- [GenomeSpy](https://genomespy.app/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomespy.png)
- [GenomePaint](https://genomepaint.stjude.cloud/) (Demos
  https://proteinpaint.stjude.org/bam/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomepaint.png)
- [covviz](https://brwnj.github.io/covviz/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/covviz.png)
- [PURPLE](https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md)
  (intermutation-distance rainfall plots/katagesis plots are not technically in
  genomic coordinates, but do indicate genomic cluster of variatnts)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/purple.png)
- [bcftools cnv](https://samtools.github.io/bcftools/howtos/cnv-calling.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_cnv.png)
- [mocha](https://github.com/freeseek/mocha) (Has a full analysis pipeline
  associated with end result visualizations)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mocha.png)
- [genevisR](https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevisr.png)
- [copynumber](https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/copynumber.png)
- [SnoopCGH](http://snoopcgh.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snoopcgh.jpg)
- [Genovar](http://genovar.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovar.png)
- [CNANorm](https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnanorm.png)
- [Orchestral](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/orchestral.png)
- [CNSpector](https://github.com/PapenfussLab/CNspector)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnspector.png)
- [sequenza](https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#plots-and-results)
  (also see https://sequenzatools.bitbucket.io/#/home)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenza.png)
- [CoveragePlotter](http://lindenb.github.io/jvarkit/CoveragePlotter.html) (See
  also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for
  multi-chromosome)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coverageplotter.png)
- [genome_coverage_plotter](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome-coverage-plotter.png)

## Static

- [BAMSnap](https://github.com/parklab/bamsnap)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamsnap.png)
- [ChIA-Pipe](https://github.com/TheJacksonLaboratory/ChIA-PIPE)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chiapipe.png)
- [CNView](https://github.com/RCollins13/CNView)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnview.jpg)
- [CNVPlot](https://github.com/dantaki/CNVplot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvplot.jpg)
- [CNVpytor](https://github.com/abyzovlab/CNVpytor)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvpytor.png)
- [DNAPlotLib](https://github.com/VoigtLab/dnaplotlib)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotlib.png)
- [ExonIntron](http://wormweb.org/exonintron)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/exonintron.png)
- [FeatureViewer](https://github.com/calipho-sib/feature-viewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/featureviewer.png)
- [Geneviz](https://jrderuiter.github.io/geneviz/usage.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviz.png)
- [Genome STRiP](http://software.broadinstitute.org/software/genomestrip/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomestrip.png)
- [GenomeTools](http://genometools.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genometools.png)
- [GenomeView](https://github.com/nspies/genomeview)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview.png)
- [genoPlotR](http://genoplotr.r-forge.r-project.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoplotr.png)
- [ggbio](http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggbio.png)
- [GGgenes](https://github.com/wilkox/gggenes)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenes.png)
- [GGsashimi](https://github.com/guigolab/ggsashimi)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggsashimi.png)
- [gtrellis](http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtrellis.png)
- [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gviz.png)
- [Hagfish](https://github.com/mfiers/hagfish/wiki/Plots)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hagfish.png)
- [HiCPlotter](https://github.com/kcakdemir/HiCPlotter)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hicplotter.jpg)
- [JVarKit/BamToSVG](http://lindenb.github.io/jvarkit/BamToSVG.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamtosvg.jpg)
- [Lollipops](https://github.com/joiningdata/lollipops)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lollipops.png)
- [Mason](http://www.yeastrc.org/mason/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mason.png)
- [Methplotlib](https://github.com/wdecoster/methplotlib)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/methplotlib.jpg)
- [Pairoscope](http://pairoscope.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pairoscope.png)
- [pauvre](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pauvre.png)
- [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks) (See also
  https://pypi.org/project/gtracks/ which is a separate project that is powered
  by pyGenomeTracks)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenometracks.png)
- [RACER](https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/racer.png)
- [RepViz](https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/repviz.png)
- [Samplot](https://github.com/ryanlayer/samplot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/samplot.jpg)
- [SashimiPlot](https://miso.readthedocs.io/en/fastmiso/sashimi.html) (See also
  rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of
  Transcript Splicing)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sashimi-plot-example.png)
- [shabam](https://github.com/dlrice/shabam)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shabam.png)
- [SparK](https://github.com/harbourlab/SparK)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spark.png)
- [Spliceclust](https://github.com/pkimes/spliceclust)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spliceclust.png)
- [Sushi](https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sushi.png)
- [svist4get](https://link.springer.com/article/10.1186/s12859-019-2706-8)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svis4get.png)
- [svv](https://github.com/ryanlayer/svv)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svv.png)
- [svviz](https://github.com/svviz/svviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz.png)
- [svviz2](https://github.com/nspies/svviz2)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz2.png)
- [trackViewer](https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackviewer.png)
- [mummer2circos](https://github.com/metagenlab/mummer2circos)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummer2circos.png)
- [cgplot](https://github.com/dfguan/cgplot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgplot.png)
- [bcftools roh](https://samtools.github.io/bcftools/howtos/roh-calling.html)
  (Plots runs of homozygosity, has interactive plot-roh.py helper too)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_roh.png)

## Gene fusion

- [Chimeraviz](https://github.com/stianlagstad/chimeraviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chimeraviz.png)
- [clinker (gene fusion software)](https://github.com/Oshlack/Clinker/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker_fusion.png)
- [arriba](https://github.com/suhrig/arriba)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/arriba.png)
- [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki)
  (Uses igv.js)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fusioninspector.png)
- [MAVIS](http://mavis.bcgsc.ca/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mavis.png)

## Alignments viewer

- [GenomeView (java app)](https://genomeview.org/content/quick-start-guide)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview_java.png)
- [pyBamView](https://mgymrek.github.io/pybamview/) (See supplementary info for
  more figures, supports padded SAM/BAM which is fairly rare)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pybamview.png)
- [Chromatic](https://chromatic.nci.nih.gov/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatic.png)
- [Gambit](http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gambit.png)
- [LookSeq](https://www.sanger.ac.uk/tool/lookseq/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lookseq.png)
- [udon](https://github.com/ocxtal/udon) (Uses an advanced data structure for
  pileup, so visually a basic example but likely just a small demo)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/udon.png)
- [wally](https://github.com/tobiasrausch/wally)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wally.png)
- [alignoth](http://htmlpreview.github.io/?https://github.com/koesterlab/alignoth/blob/main/examples/plot.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignoth.png)
- [gw](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gw.png)
- [DrukBam](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/drukbam.png)
- [bamscope](https://github.com/jslfree080/bamscope)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscope.png)

## Comparative

- [GSSPlayground](https://github.com/orangeSi/GSSplayground)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gssplayground.png)
- [Aequatus](https://github.com/TGAC/Aequatus)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aequatus.png)
- [AliTV](https://alitvteam.github.io/AliTV/d3/AliTV.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitv.png)
- [Artemis comparison tool (ACT)](https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/artemis_act.png)
- [Biodalliance comparative demo](http://biodalliance.org/dev/test-comparative.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance_comparative.png)
- [Chromatiblock](https://github.com/mjsull/chromatiblock)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatiblock.png)
- [CMap](http://gmod.org/wiki/CMap)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmap.jpg)
- [CoGe](https://genomevolution.org/coge/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coge.png)
- [Comparative assembly hub / "snake track"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/comparative_assembly_hub.png)
- [CrossBrowse](https://github.com/shenkers/CrossBrowse)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/crossbrowse.png)
- [CVit](https://sourceforge.net/projects/cvit/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvit.png)
- [Cvit.js](https://github.com/LegumeFederation/cvitjs)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvitjs.png)
- [EasyFig](https://mjsull.github.io/Easyfig/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/easyfig.png)
- [GBrowse_syn](http://gmod.org/wiki/GBrowse_syn)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse_syn.png)
- [Genome Context Viewer](https://www.legumefederation.org/gcv/phytozome_10_2/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_context_viewer.png)
- [Genome-plots-processing](https://github.com/filip-husnik/genome-plots-processing)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_plots_processing.png)
- [Genomicus](https://www.genomicus.biologie.ens.fr/genomicus/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicus.png)
- [gggenomes](https://github.com/thackl/gggenomes)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenomes.png)
- [GIVE](https://zhong-lab-ucsd.github.io/GIVE_homepage/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/give_hic.png)
- [mauve-viewer](https://github.com/nconrad/mauve-viewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mauve_viewer.png)
- [MCScan (python version)](<https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)>)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscan_python.png)
- [MCScanX](https://github.com/wyp1125/MCScanX)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscanx.png)
- [mGSV (multiple genome synteny viewer)](https://github.com/kashmatic/mGSV)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgsv.jpg)
- [MizBee](http://www.cs.utah.edu/~miriah/mizbee/Overview.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mizbee.jpg)
- [Multiple genome viewer](http://www.informatics.jax.org/mgv/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgv.png)
- [OMA local synteny browser](https://omabrowser.org/oma/synteny/ADH1A_HUMAN/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/oma.png)
- [pafr](https://github.com/dwinter/pafr)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pafr.png)
- [Parasight](https://baileylab.brown.edu/parasight/galframe.html) (Examples at
  https://ratparalogy.gs.washington.edu/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/parasight.png)
- [progressiveMauve viewer](http://darlinglab.org/mauve/user-guide/viewer.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/progressive_mauve.png)
- [SyMap](http://www.agcol.arizona.edu/software/symap/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/symap.png)
- [Synima](https://github.com/rhysf/Synima)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synima.png)
- [Synteny browser](https://github.com/TheJacksonLaboratory/syntenybrowser)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jax_synteny_browser.png)
- [SynTView](http://hub18.hosting.pasteur.fr/SynTView/documentation/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntview.png)
- [SynVisio](https://synvisio.github.io/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synvisio.png)
- [Tripal MapViewer](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tripal_mapviewer.png)
- [VISTA browser](http://pipeline.lbl.gov/cgi-bin/gateway2)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vista.png)
- [XMatchView](https://www.bcgsc.ca/resources/software/xmatchview)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/xmatchview.png)
- [LinearDisplay.pl](https://github.com/JCVenterInstitute/LinearDisplay) (readme
  says to cite this paper)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lineardisplay.png)
- [FastANI](https://github.com/ParBLiSS/FastANI)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fastani.jpg)
- [clinker](https://github.com/gamcil/clinker)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker.png)
- [RectChr](https://github.com/BGI-shenzhen/RectChr)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rectchr.png)
- [pretzel](https://github.com/plantinformatics/pretzel)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretzel.png)
- [PipMaker](http://pipmaker.bx.psu.edu/pipmaker/) (See also MultiPipMaker
  http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pipmaker.png)
- [WGDI](https://github.com/SunPengChuan/wgdi)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgdi.png)
- [BRIG](http://brig.sourceforge.net)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/brig.jpg)
- [GENESPACE](https://github.com/jtlovell/GENESPACE/) (Includes a powerful
  analysis pipeline, worth reading the paper)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genespace.png)
- [miropeats](http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/)
  (image from 2021 paper
  https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/miropeats.png)
- [syntenyPlotteR](https://github.com/marta-fb/syntenyPlotteR)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyplotter.png)
- [chromoMap](https://lakshay-anand.github.io/chromoMap/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromomap.png)
- [SafFire](https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/saffire.png)
- [SimpleSynteny](https://www.dveltri.com/simplesynteny/about.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/simplesynteny.jpg)
- [Cinteny](http://cinteny.cchmc.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cinteny.png)
- [AutoGraph](http://autograph.genouest.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/autograph.png)
- [EvolutionHighway](http://eh-demo.ncsa.illinois.edu/) (The 'evolutionary
  highway' image type is reproduced in some other packages e.g.
  https://github.com/marta-fb/syntenyPlotteR, paper
  https://doi.org/10.1126/science.1111387)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/evolutionaryhighway.jpg)
- [Smash++](https://github.com/smortezah/smashpp)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/smashpp.png)
- [plotsr](https://github.com/schneebergerlab/plotsr) (Blurs the line between
  synteny and SV visualization, a good thing! see also
  https://github.com/schneebergerlab/syri)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotsr.png)
- [GenomeMatcher](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomematcher.png)
- [SynBrowse](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synbrowse.png)
- [Sybil](http://sybil.sourceforge.net/) (Download
  https://sourceforge.net/projects/sybil/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sybil.png)
- [SyntenyPortal](http://bioinfo.konkuk.ac.kr/synteny_portal/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyportal.png)
- [CHROMEISTER](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromeister.png)
- [r2cat](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/r2cat.jpeg)
- [SequenceSurveyor](https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequencesurveyor.png)
- [BactoGENIE](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bactogenie.png)
- [PSAT](http://www.nwrce.org/psat)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/psat.png)
- [TreeBrowser (MicrobesOnline)](http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/treegenome.png)
- [Combo](undefined) (Based on the tool 'Argo')
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/combo.png)
- [GenomicBreaks](https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicbreaks.png)
- [GenomeSyn](https://github.com/jmsong2/GenomeSyn)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomesyn.png)
- [CrowsNest](https://pgsb.helmholtz-muenchen.de/crowsnest/help.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/crowsnest.png)
- [GGisy](https://github.com/Sanrrone/GGisy)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggisy.png)
- [multiGenomicContext](https://github.com/Sanrrone/multiGenomicContext)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/multicontext.png)
- [AccuSyn](https://accusyn.usask.ca/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/accusyn.png)
- [pyGenomeViz](https://github.com/moshi4/pyGenomeViz) (See also
  https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz
  https://github.com/moshi4/plot_genome_align_fig)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenomeviz.png)
- [ShinySyn](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinysyn.png)
- [NCBI CGV](https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgv.png)
- [asynt](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asynt.png)
- [NGenomeSyn](undefined) (See also RectChr)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngenomesyn.png)
- [chromsyn](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromsyn.png)
- [syntR](https://www.samuklab.com/syntR/articles/syntr_tutorial.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntr.png)
- [GCSnap](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcsnap.png)
- [ModDotPlot](https://github.com/marbl/ModDotPlot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/moddotplot.png)
- [odp (oxford dot plots)](https://github.com/conchoecia/odp) (Pub is not for
  visualization tool, but it is suggested to cite this paper)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/odp.png)

## Single cell

- [Millefy](https://github.com/yuifu/millefy)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/millefy.png)
- [gingko](http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingko.jpeg)
- [copykat](https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/copykat.png)
- [scCNV_heatmap](https://github.com/StefanKurtenbach/scCNV_heatmap)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sccnv_heatmap.png)
- [casper](https://github.com/akdess/CaSpER)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/casper.png)
- [ArchR](https://www.archrproject.com/articles/Articles/tutorial.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/archr.png)
- [numbat](https://kharchenkolab.github.io/numbat/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/numbat.png)
- [MosaicCatcher pipeline](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaicatcher.png)

## GWAS

- [PureScript genetics browser](https://github.com/chfi/purescript-genetics-browser)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/purescript.png)
- [Locuszoom](http://locuszoom.org/) (Also see locuszoom.js
  http://locuszoom.org/locuszoomjs.php)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoom.png)
- [LDBlockShow](https://github.com/BGI-shenzhen/LDBlockShow)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ldblockshow.png)
- [ggplot2 manhattan plot](https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/)
  (This is not a preconfigured tool but a blog post tutorial with tidy data and
  ggplot2)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggplot2_manhattan.png)
- [CMPlot](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmplot.png)
- [GeneticsMakie.jl](https://github.com/mmkim1210/GeneticsMakie.jl)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneticsmakie.png)

## Dotplot

- [shinyChromosome](http://150.109.59.144:3838/shinyChromosome/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinychromosome.png)
- [D-GENIES](http://dgenies.toulouse.inra.fr/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dgenies.png)
- [Delly-maze](https://github.com/dellytools/maze) (see also
  https://www.gear-genomics.com/maze/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/maze.png)
- [Discoplot](https://github.com/mjsull/DiscoPlot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/discoplot.png)
- [Dot](https://dot.sandbox.bio/) (Python data preparation script)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dot.png)
- [Dotlet](https://dotlet.vital-it.ch/) (The original publication was 2000 but
  updated ~2020 with reactjs)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotlet.png)
- [Dotplot (chirimoyo)](https://chirimoyo.ac.uma.es/bitlab/portfolio/dotplot/)
- [iLambda/Dotplot](https://github.com/iLambda/dotplot)
- [dotPlotly](https://github.com/tpoorten/dotPlotly/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotplotly.png)
- [Dottup](https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup) (also seen
  here
  http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dottup.png)
- [FlexiDot](https://github.com/molbio-dresden/flexidot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/flexidot.png)
- [Gepard](http://cube.univie.ac.at/gepard)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gepard.jpeg)
- [Jdot](https://github.com/LyonsLab/jdot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jdot.png)
- [last-dotplot](https://gitlab.com/mcfrith/last)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/last_dotplot.png)
- [mcutils](https://github.com/mchaisso/mcutils)
  (https://twitter.com/mjpchaisson/status/1040363992206569472)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcutils_dotplot.jpeg)
- [Minidot](https://github.com/thackl/minidot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/minidot.png)
- [Mummer-idotplot](https://github.com/ryought/mummer-idotplot)
- [Mummerplot](http://mummer.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot.png)
- [ggplot2 mummerplot](https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot_ggplot2.png)
- [Redotable](https://github.com/s-andrews/redotable)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/redotable.png)
- [syntenyPlotByR](https://github.com/shingocat/syntenyPlotByR)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synteny_plot_by_r.png)
- [Dotter](https://sonnhammer.sbc.su.se/Dotter.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotter.png)
- [JGI/IMG](https://img.jgi.doe.gov/) (Dotplot use MUMmer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jgiimg.png)
- [MashMap](https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mashmap.png)
- [oxford-plots](https://github.com/jherrero/oxford-plots) (Has nice description
  of a synteny pipeline here
  https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/oxford.png)
- [DAGchainer](http://dagchainer.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dagchainer.png)
- [local-rearrangements](https://github.com/mcfrith/local-rearrangements) (Can
  color dotplots with annotations for e.g. exons, transposons, low complexity
  regions. See also last-dotplot. Nice figure using it here
  https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/local-rearrangements.png)

## Gene structure

- [TnT](https://tnt.marlin.pub/articles/introduction)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tnt.png)
- [Apollo aka WebApollo](https://genomearchitect.readthedocs.io/en/latest/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/webapollo.jpg)
- [ggtranscript](https://github.com/dzhang32/ggtranscript)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtranscript.png)

## Microbiology

- [Edinburgh-Genome-Foundry/DnaFeaturesViewer](https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer)
  (See also https://github.com/Edinburgh-Genome-Foundry/Caravagene)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnafeaturesviewer.png)
- [GeneViTo](http://athina.biol.uoa.gr/bioinformatics/GENEVITO/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevito.jpg)
- [GECO](http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geco.png)
- [GeCoViz](https://gecoviz.cgmlab.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gecoviz.png)
- [clonifier](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clonifier.png)

## Graph

- [AGB assembly graph browser](https://almiheenko.github.io/AGB/index.html)
- [Bandage](https://github.com/rrwick/Bandage/) (See also BandageNG
  https://github.com/asl/BandageNG)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bandage.png)
- [gfaestus](https://github.com/chfi/gfaestus) (See demo video displaying GFF3
  annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaestus.png)
- [graphgenomeviewer](https://cmdcolin.github.io/graphgenomeviewer/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphgenomeviewer.png)
- [MoMi-G](https://github.com/MoMI-G/MoMI-G)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/momig.png)
- [odgi draw + odgi viz + odgi inject](https://odgi.readthedocs.io/en/latest/index.html)
  (Example from https://github.com/pangenome/pggb, see also gene arrow map
  https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/odgi.png)
- [sequence tube map](https://github.com/vgteam/sequenceTubeMap)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequence_tube_map.png)
- [Shasta](https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph)
  (Uses graphviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shasta.png)
- [LINX](https://github.com/hartwigmedical/hmftools/blob/master/linx/README.md)
  (part of the PURPLE/GRIDSS/LINX pipeline)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/linx.png)
- [GfaViz](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaviz.png)
- [panGraphViewer](https://github.com/TF-Chan-Lab/panGraphViewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pangraphviewer.jpg)
- [IGGE](https://github.com/immersivegraphgenomeexplorer/IGGE) (Not open source)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igge.png)
- [ctag](undefined) (See also hygene
  https://github.com/ProgrammingLife2017/hygene)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ctag.png)
- [PGR-TK](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgrtk.png)
- [VRPG](https://github.com/codeatcg/VRPG)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vrpg.png)

## SV

- [gGnomes](https://github.com/mskilab/gGnome)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomesr.png)
- [gGnomes.js](https://github.com/mskilab/gGnome.js)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomes.png)
- [Ribbon](http://genomeribbon.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeribbon.png)
- [Gremlin](http://compbio.cs.brown.edu/projects/gremlin/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gremlin.png)
- [InGAP-SV](http://ingap.sourceforge.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ingap_sv.png)
- [Introgression browser](https://git.wageningenur.nl/aflit001/ibrowser)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/introgression_browser.png)
- [SplitThreader](http://splitthreader.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/splitthreader.png)
- [SMRT View](http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm)
  (wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/smrtview.png)
- [asgart](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asgart.png)
- [NeoLoopFinder](https://github.com/XiaoTaoWang/NeoLoopFinder)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/neoloopfinder.png)
- [SVPV](https://github.com/VCCRI/SVPV)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svpv.jpg)
- [AmpliconArchitect](https://github.com/virajbdeshpande/AmpliconArchitect) (The
  term amplicon refers essentially to extrachromosomal DNA in cancer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ampliconarchitect.png)
- [bigly](https://github.com/brentp/bigly)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigly.png)
- [vcf2circos](https://github.com/bioinfo-chru-strasbourg/vcf2circos) (Based on
  PCircos https://github.com/CJinny/PCircos)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcf2circos.png)
- [ReConPlot](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/reconplot.png)

## Text based

- [Alan](https://github.com/mpdunne/alan)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alan.png)
- [Alv](https://github.com/arvestad/alv)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alv.png)
- [ASCIIGenome](https://github.com/dariober/ASCIIGenome)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asciigenome.png)
- [Bamcov](https://github.com/fbreitwieser/bamcov)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamcov.png)
- [BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
- [Hapviz](https://github.com/ekg/hapviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hapviz.png)
- [plotReads](http://campuspress.yale.edu/knightlab/ruddle/plotreads/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotreads.png)
- [Rna Alignment Viewers (Colorstock, SScolor, Ratón)](http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rnaalignment.png)
- [Sam2pairwise](https://github.com/mlafave/sam2pairwise)
- [Samtools depth visualization](https://twitter.com/yokofakun/status/1178686978541441025)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/depthplot.png)
- [Samtools tview](http://www.htslib.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tview.png)
- [SvABA](https://github.com/walaj/svaba#alignmentstxtgz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svaba.png)
- [VizAln (from HipSTR)](https://github.com/tfwillems/HipSTR)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipstr.png)
- [pileuppy](https://gitlab.com/tprodanov/pileuppy)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileuppy.png)

## Circular

- [Anvio](https://peerj.com/articles/1319/)
- [BioCircos.js](http://bioinfo.ibp.ac.cn/biocircos/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biocircos.png)
- [Circleator](http://jonathancrabtree.github.io/Circleator/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circleator.png)
- [circlize](https://github.com/jokergoo/circlize)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circlize.jpeg)
- [Circos](http://circos.ca/) (the github repo is not up to date with the latest
  code)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circos.png)
- [CircosJS](https://github.com/nicgirault/circosJS)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circosjs.png)
- [DNAPlotter](https://www.sanger.ac.uk/science/tools/dnaplotter)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotter.jpg)
- [GenomeProjector](https://github.com/gaou/g-language/wiki)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/glanguage.jpg)
- [JupiterPlot](https://github.com/JustinChu/JupiterPlot)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jupiterplot.png)
- [OGDRAW](https://chlorobox.mpimp-golm.mpg.de/OGDraw.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ogdraw.png)
- [Gview](https://server.gview.ca/examples)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gview.png)
- [RegulomeExplorer](http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cancerregulome.png)
- [CGView](http://cgview.ca/) (See also CGView comparison tool and other related
  https://paulstothard.github.io/cgview_comparison_tool/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgview.png)
- [pyCircos](https://github.com/ponnhide/pyCircos) (See also
  https://github.com/ponnhide/plasmidviewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycircos.png)
- [pyCirclize](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycirclize.png)
- [OmicCircos](http://bioconductor.org/packages/release/bioc/html/OmicCircos.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/omiccircos.png)
- [genoVi](https://github.com/robotoD/GenoVi)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovi.png)

## Synthetic biology

- [seqviz](https://github.com/Lattice-Automation/seqviz#viewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqviz.png)
- [ApE (a plasmid editor)](https://jorgensen.biology.utah.edu/wayned/ape/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aplasmideditor.png)
- [Chopchop](http://chopchop.cbu.uib.no/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chopchop.png)
- [plasmapR](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plasmapr.png)

## Special-purpose

- [Apollo](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/apollo.jpg)
- [D3GB](http://d3gb.usal.es/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/d3gb.png)
- [DNASkittle](https://www.dnaskittle.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaskittle.png)
- [EaSeq](https://easeq.net/screenshots/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/easeq.png)
- [FluentDNA](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203487/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fluentdna.jpeg)
- [Gnomad browser](https://github.com/macarthur-lab/gnomadjs)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gnomad.png)
- [Hawkeye](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hawkeye.png)
- [IslandViewer and IslandPlot](https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565)
  (web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/islandplot.png)
- [MagicViewer](http://bioinformatics.zj.cn/magicviewer/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/magicviewer.jpeg)
- [Panoptes](https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panoptes.png)
- [MapView](https://sites.google.com/site/wjwdavy/) (links in original paper are
  dead, but URL provided here works)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mapview.jpg)
- [NGB](https://github.com/epam/NGB)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngb.png)
- [SeqCover](https://brentp.github.io/seqcover/#gene=AIFM1)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqcover.png)
- [SEQing](https://github.com/malewins/SEQing)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqing.png)
- [SFARI](https://gene.sfari.org/database/human-gene/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sfari.jpg)
- [Short read assembly browser](https://rapdb.dna.affrc.go.jp/AssemblyBrowser2/index.html?ref=%22chr01%22&run_id=%22G4toI1%22&start=%22234780%22&end=%22236631%22)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/short_read_assembly_browser.png)
- [SNPitty](https://bitbucket.org/ccbc/snpitty/src/master/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpitty.jpg)
- [Staden](https://sourceforge.net/projects/staden/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/staden.png)
- [TASUKE](https://ricegenome.dna.affrc.go.jp/) (info about multi-genome-browser
  https://tasuke.dna.affrc.go.jp/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tasuke.png)
- [TE-nest](undefined) (this was an online tool that does not appear to exist
  anymore see
  https://web.archive.org/web/20170712104431/http://www.plantgdb.org/tool/TEnest/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tenest.jpg)
- [Transposcope](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/transposcope.png)
- [UGENE](http://ugene.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ugene.png)
- [Varsome](<https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET>)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/varsome.png)
- [Vials](http://vials.io/)
- [wasm bigwig demo browser](https://shk656461.github.io/index.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasm_bigwig.png)

## Expression

- [GTEX Locus browser](https://gtexportal.org/home/locusBrowserPage/ACTN3)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtex_locus.png)

## Population

- [GWAS catalog browser](https://www.ebi.ac.uk/gwas/variants/rs1558902)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gwascatalog.png)
- [Human genome dating](https://human.genome.dating/region/chr1_13250000) (made
  with vega/d3)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/human_genome_dating.png)
- [PopSV](https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/popsv.png)
- [SWAV](http://swav.popgenetics.net/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/swav.png)
- [Haploview](https://www.broadinstitute.org/haploview/haploview)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/haploview.png)
- [pixy](https://pixy.readthedocs.io/en/latest/plotting.html#a-genome-wide-plot-of-summary-statistics)
  (The link in readthedocs shows a nice general purpose way to plot
  multi-chromosome plots in ggplot2 with facet grid. Alternative methods for
  multi-chromosome plots shown by the manhattan ggplot2 tutorial
  (https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses
  cumulative bp instead of facet_grid))
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pixy.png)

## Assembly QC

- [Icarus QUAST](http://quast.sourceforge.net/icarus.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/icarus.png)

## Exotic

- [BigTop](https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigtop.png)
- [Cylindrical alignment app](https://sourceforge.net/projects/cylindrical-alignment-app/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cylindrical_alignment_viewer.png)
- [sockeye](https://www.bcgsc.ca/resources/software/sockeye)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sockeye.jpg)
- [spinteny](https://github.com/skinner/spinteny)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spinteny.png)

## Epigenomics

- [Chip Monk](http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/) (Also
  see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipmonk.png)
- [Chipster](https://chipster.csc.fi/) (Copy number tutorial
  https://chipster.csc.fi/manual/cn-tutorial.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipster.jpg)
- [cisGenome Browser](https://jhui2014.github.io/browser/screenshots.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cisgenome.png)
- [Epilogos](https://epilogos.altius.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/epilogos.jpg)
- [Epiviz](https://epiviz.github.io/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/epiviz.png)
- [HiPiler](http://hipiler.higlass.io)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipiler.png)
- [Juicebox](https://github.com/aidenlab/Juicebox)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/juicebox.jpg)
- [Juicebox.js](http://www.igv.org/doc/juiceboxjs.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/juiceboxjs.jpg)
- [Peax](https://github.com/Novartis/peax)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/peax.png)
- [CoolBox](undefined) (fork of pyGenomeTracks)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coolbox.png)
- [JBR](https://artyomovlab.wustl.edu/jbr/2018_h3k27ac_aging/) (Not open source,
  at least not on github)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbr.png)
- [python-genome-browser aka pygbrowse](https://github.com/phageghost/python-genome-browser/blob/master/pygbrowse_demonstration.ipynb)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygbrowse.png)

## Ideogram

- [eweitz/Ideogram](https://github.com/eweitz/ideogram)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/eweitz_ideogram.png)
- [Ideogram](https://github.com/RCollins13/HumanIdiogramLibrary)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rcollins_ideogram.png)
- [Ideoplot](https://github.com/mchaisso/Ideoplot)
- [karyoploteR](https://github.com/bernatgel/karyoploteR)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyoploter.png)
- [KaryotypeSVG](https://github.com/andreasprlic/karyotypeSVG)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyotypesvg.png)
- [NCBI Genome Decoration](undefined) (Was located at
  https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbi_genome_decoration.png)
- [UCSC Genome Graphs](http://genome.ucsc.edu/cgi-bin/hgGenome)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc_genome_graph.png)
- [genomegraphs](http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomegraphs.png)
- [IdeoViz](https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideoviz.png)
- [Flash Gviewer](http://gmod.org/wiki/Flashgviewer/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/flashgviewer.png)
- [Ideogram viewer](https://bioinformatics.mdanderson.org/public-software/ideogramviewer/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideogramviewer.png)
- [chromPlot](https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromplot.png)
- [PhenoGram](https://ritchielab.org/software/phenogram-downloads) (Can be web
  server or download)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/phenogram.png)
- [RIdeogram](https://github.com/TickingClock1992/RIdeogram)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rideogram.png)
- [tagore](https://github.com/jordanlab/tagore)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tagore.png)
- [ezcharts](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ezcharts.png)

## Mobile

- [iGenomics](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igenomics.png)

## Pangenome

- [Pan-Tetris](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pantetris.png)
- [Panacaea](https://github.com/JCVenterInstitute/PanACEA)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panacaea.png)
- [Panache](https://github.com/SouthGreenPlatform/panache)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panache.png)
- [panX](http://pangenome.tuebingen.mpg.de/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panx.jpeg)
- [RPAN (3kricedb)](http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rpan.png)
- [PGAP-X](https://pgapx.zhaopage.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgapx.png)
- [PGV](https://github.com/ucrbioinfo/PGV)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv.png)
- [Phandango](https://jameshadfield.github.io/phandango/#/examples)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/phandango.png)

## Protein

- [Protael](http://sanshu.github.io/protaelweb/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/protael.png)
- [ProteinPaint](https://pecan.stjude.cloud/proteinpaint)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/proteinpaint.png)
- [pViz](https://github.com/Genentech/pviz)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pviz.jpg)
- [Aquaria](http://aquaria.ws/Q9HD67/5i0i/A)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aquaria.png)
- [nightingale/protvista](https://ebi-webcomponents.github.io/nightingale/#/msa)
  (Used on InterProScan website https://www.ebi.ac.uk/interpro/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nightingale.png)
- [drawProteins](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/drawprotein.png)
- [IBS (Illustrator for Biological Sequences)](http://ibs.biocuckoo.org/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ibs.jpg)
- [PFAM generate_graphic](https://pfam.xfam.org/generate_graphic) (Also see
  guide here https://pfam.xfam.org/help#tabview=tab10)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pfam.png)
- [Prosite/MyDomains](https://prosite.expasy.org/mydomains)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/prosite.png)
- [TogoStanza Protein Browser](https://db-dev.jpostdb.org/ts/stanza/protein_browser/help.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/togostanza.png)

## Heatmap

- [UCSC Xena](https://xena.ucsc.edu/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/xena.png)
- [VIVA](https://www.biorxiv.org/content/10.1101/589879v1.full.pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/viva.png)

## Repeats

- [REPAVER](https://gitlab.com/gringer/bioinfscripts/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/repaver.jpg)
- [GraphAlignmentViewer](https://github.com/Illumina/GraphAlignmentViewer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphalignmentviewer.png)
- [REViewer](https://github.com/Illumina/REViewer) (See also
  GraphAlignmentViewer, similar look and from illumina also)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/reviewer.png)
- [StainedGlass](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/stainedglass.png)
- [SODA](https://sodaviz.org/) (Describes itself as a low-level library to
  create larger applications with)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/soda.png)
- [TRVZ (TRGT tandem repeat genotyping visualizer)](trvz.png)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trvz.png)

## Historical

- [Internet Contig Explorer](https://www.bcgsc.ca/resources/software/ice)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/internet_contig_explorer.jpg)

## QC

- [ALVIS (chimeric alignment viewer)](https://github.com/SR-Martin/alvis)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis_chimeric.png)
- [vcfR](https://knausb.github.io/vcfR_documentation/) (image shows chromoqc
  output)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfr.png)

## Methylation

- [NanoMethViz](http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nanomethviz.png)
- [AnnoJ](https://brainome.ucsd.edu/howto_annoj.html) (See list of instances of
  the browser here https://ecker.salk.edu/genome-browser/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/annoj.png)
- [modbamtools](https://github.com/rrazaghi/modbamtools)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/modbamtools.png)

## Phylogenetics

- [Nextclade](https://clades.nextstrain.org/) (Related usage on nextstrain app
  also)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nextclade.png)
- [Gingr](https://harvest.readthedocs.io/en/latest/content/gingr.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingr.png)
- [Taxonium](https://taxonium.org) (Genome variation visualisation in Taxonium
  is provided by the 'Treenome Viewer':
  https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/taxonium.png)

## Long reads

- [methylartist](https://github.com/adamewing/methylartist)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/methylartist.png)

## Assembly

- [vega](http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL)
  (Mentioned in
  https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also
  note: vega standards for vertebrate genome annotation database)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vega.png)
- [MIRA](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html)
  (orig paper also describes mira here
  http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mira.png)

## Coverage

- [wiggleplotr](http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wiggleplotr.png)
- [Trackplot (R)](https://github.com/PoisonAlien/trackplot) (suggests citing
  bwtool linked here)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot.png)
- [signac](https://github.com/timoast/signac/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/signac.png)
- [ggcoverage](https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggcoverage.png)
- [BAMdash](https://github.com/jonas-fuchs/BAMdash/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamdash.png)

## Splicing

- [splicejam](https://github.com/jmw86069/splicejam)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/splicejam.png)
- [Slinker](https://github.com/Oshlack/Slinker) (See also, clinker (gene fusion
  software))
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/slinker.png)

## Hi-C

- [Plotgardener](https://github.com/PhanstielLab/plotgardener/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotgardener.png)
- [gcMapExplorer](https://github.com/rjdkmr/gcMapExplorer)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcmapexplorer.png)
- [PretextView](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretextview.jpg)

## Deadlink

- [VAMP](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vamp.jpg)
- [CGH-Explorer](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cghexplorer.jpg)
- [DNAVis](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnavis.png)

## BLAST

- [SequenceServer](https://sequenceserver.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenceserver.png)

## Academic license

- [Consed](http://bozeman.mbt.washington.edu/consed/consed.html)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/consed.png)

## Local ancestry

- [fineSTRUCTURE aka ChromoPainter](http://www.paintmychromosomes.com/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/finestructure.png)
- [MOSAIC](https://maths.ucd.ie/~mst/MOSAIC/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaic.png)

## Variation

- [snpit](https://github.com/aineniamh/snipit)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpit.png)
- [vcfPlotein](https://vcfplotein.liigh.unam.mx/#/)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfplotein.png)
- [NucFreq](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucfreq.png)

## Chromosome painting

- [GeMo](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gemo.png)

## Text-based

- [rich-msa](undefined)
  [(img)](https://cmdcolin.github.io/awesome-genome-visualization/richmsa.png)

# Other lists

- [Awesome Bioinformatics](https://github.com/danielecook/Awesome-Bioinformatics)
- [Genocat](http://genocat.tools/) large collection of genomic visualizations
  with great review paper accompaniment
  https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727
- [awesome-biological-visualizations](https://github.com/keller-mark/awesome-biological-visualizations)

Send in PRs for more stuff!

## License

This README.md and TOOLS.json are CC0
https://creativecommons.org/publicdomain/zero/1.0/

The website code is MIT