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cmdcolin/awesome-genome-visualization: A list of interesting genome browser and genome visualization programs

cmdcolin/awesome-genome-visualization: A list of interesting genome browser and genome visualization programs

12 hours ago
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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 BlueSky https://bsky.app/profile/awesomegenomeviz.bsky.social or Mastodon account https://genomic.social/@awesomegenomevisualization

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, ggplot2, matplotlib, and (the elephant in the room: coding agents, but careful with these, they can hamper your learning if you become overly reliant on them) make this much easier! But also consider making your visualization code re-usable for the wider community! And feel free to send PRs for more tools!

Finally, at least 68% (372/543) tools in this list have written publications for their tools. They went through the effort to write it up, cite these tools!!

New rule: 2026-10-11 I will no longer be accepting tools without source available. I don't want feel inspired to share source-not-available vibe-coded tools in this repo. Rare exceptions may be made for commercial vendors that have unique functionality in line with pre-existing commercially tagged tools, or certain web based tools (e.g. my Silo tag), where sharing the code is not feasible.

Genome browser

  • ABrowse (genome browser) (Had integrations with BioMart, Taverna)
(img) (img) (img) (img) (img) (img) (img) (img) browser: conversational agents drive the view and run BLAST, primer design, and structure lookups; MCP server and plugin architecture included) (img) (img) (img) (img) (img) (img) https://doi.org/10.1101/gr.403602) (img) (img) (img) (img) (img) academic use) (img)
  • Gosling (Comparative views are limited to band
tracks, see https://gosling.js.org/?example=BAND) (img)
  • gtracks (Powered by pyGenomeTracks)
(img) (img) (img) (img) (img)
  • JBR (Not open source,
at least not on github) (img)
  • JBrowse (See also JBrowse plugin registry
https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron) (img) https://jbrowse.org/jb2/gallery) (img) 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) (img) https://github.com/nucleome) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) 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) (img)

Accessibility

  • VIJB (Companion to JBrowse that makes
genome browsing usable for visually impaired people)

Annotation

(img)

Assembly QC

(img) (img) (img) (img) (img) (orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf) (img) (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)

BLAST

(img)

Chromatogram

  • ab1lens (Free, browser-based Sanger / .ab1
chromatogram viewer. View and compare raw vs analyzed traces and basecalls, align a read to a reference to find mismatches, and export a high-resolution image. Runs entirely client-side — data never leaves the browser.) (img)

Circular

genomes, MAGs and multi-genome synteny) (img) (img) (img) (img)
  • CGView (See also CGView comparison tool and other related
https://paulstothard.github.io/cgview_comparison_tool/) (img) (img) (img) (img) (img)
  • Circos (no official github to my knowledge)
(img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) https://github.com/ponnhide/plasmidviewer) (img) (img) (img) (img) metagenome-assembled genomes at once, highlighting virulence and antimicrobial resistance genes) (img)

CNV

(img) (img) (img)
  • CGH-Explorer
(img) (img) (img) (img) (img) (img) (img) (img) (img) also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for multi-chromosome) (img) (img) (img) (img) https://proteinpaint.stjude.org/bam/) (img) (img) (img)
  • mocha (Has a full analysis pipeline
associated with end result visualizations) (img)
  • Orchestral
(img) (intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variants) (img) (img) (also see https://sequenzatools.bitbucket.io/#/home) (img) (img) (img) (img)

Comparative genomics

  • Combo (Based on the tool 'Argo')
(img) (img) https://ratparalogy.gs.washington.edu/) (img)

Coverage

(img)
  • dep (Can handle very deep coverage)
(img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img)

Dotplot

(img) (img) (img) (img) (img) (img) https://www.gear-genomics.com/maze/) (img) (img)
  • DNAVis
(img)
  • Dot (Python data preparation script)
(img)
  • Dotlet (The original publication was 2000 but
updated ~2020 with reactjs) (img) (img) (img) here http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf) (img) (img) (img) (img) (img)
  • Hobrac (Finds a reference genome
by homology and draws dotplots against it, including BUSCO-gene dotplots) (img) (img) (img) (img) 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) (img) (Also has 2024 citation here https://onlinelibrary.wiley.com/doi/10.1002/imt2.211) (img) (https://twitter.com/mjpchaisson/status/1040363992206569472) (img) (img) (img) (img) visualization tool, but it is suggested to cite this paper) (img) of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img)

Epigenomics

(img) see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) (img) https://chipster.csc.fi/manual/cn-tutorial.pdf) (img) (img) (img) (img) (img) (img) (img)

Expression

(img) rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of Transcript Splicing) (img)

Gene fusion

https://www.agfusion.app/ for web based version) (img) (img) (img) (img) (Uses igv.js) (img) (img) (img)

Gene order

  • BactoGENIE
(img) (img) (img) (img) (img) (img) (img) (img) (img) (img)

Gene structure

(URL is an archive.org link) (img) (img) http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963 doesn't work anymore) (img) (img) (img) (img) (img) original figures for the human Celera genome) (img) (img) (img)

Genetic map

(img) (img)

Genome graph

(img) https://github.com/asl/BandageNG) (img) the browser. Highlights walks and reads one region at a time from a whole-genome pangenome. Demo https://jbrowse.org/demos/bandagejs/) (img)
  • ctag (See also hygene
https://github.com/ProgrammingLife2017/hygene) (img)
  • gfaestus (See demo video displaying GFF3
annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4) (img) (img) (img) layers, laid out as Bandage lays them out) (img) tube maps as ggplot2 layers. See also sequenceTubeMap https://github.com/vgteam/sequenceTubeMap) (img) (img)
  • IGGE (Not open source)
(img) (img) (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) (img) (img) tool for layout and visual analysis of pangenome graphs, with BLAST search over segments. Demo http://pg2.cs.bilkent.edu.tr) (img) (img) (img) https://github.com/cmdcolin/sequenceTubeMap, a fork with modernizations) (img) (img) (Uses graphviz) (img) assembly graph viewer in the browser, rendered with WebGL. Demo https://mdondrup.github.io/SloppyyGFA/) (img) (img) (img) (img) (img)

GWAS

(img) (img) (This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2) (img) (img) that color variants by LD with several index variants at once, plus locus compare plots. Demo https://locusblend.wustl.edu) (img) (img) (img) (img)

Heatmap

(img) (img)
  • vitessce (Uses higlass, web based with (optional)
Python and R integrations, not all visualization are 'genome coordinates') (img) (img)

Hi-C

(img) (img) (img) (img) Plotgardener App, a graphical interface https://github.com/rishabhsvemuri/ThePlotgardenerApp) (img) (img) https://pypi.org/project/gtracks/ which is a separate project that is powered by pyGenomeTracks) (img) (img)

Ideogram

(img) (img) https://github.com/rraadd88/beditor) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img) (img)
  • NCBI Genome Decoration (Was located at
https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023) (img) server or download) (img) (img) (img) (img) (img) (img) (img)

K-mer

(img)

Linear

(See also https://github.com/Edinburgh-Genome-Foundry/Caravagene) (img) (img) (img) (img) (img) (img) says to cite this paper) (img) (img)

Local ancestry

(img) (img) (img)
  • ... (README truncated for length)

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