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
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!
- Genoverse (img)
- BasePlayer (img)
- Celera genome browser (img)
- IGB (img)
- IGV (img)
- Savant (img)
- Tablet (img)
- Biodalliance (img)
- Ensembl genome browser (img)
- Ensembl genome browser 2020 edition (img)
- GBrowse 2 (Original gbrowse paper https://doi.org/10.1101/gr.403602) (img)
- GenomeMaps (img)
- Gosling (img)
- HiGlass (img)
- IGV.js (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)
- JBrowse 2 (See gallery for more examples https://jbrowse.org/jb2/gallery) (img)
- Kero-BROWSE (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)
- NCBI Genome Data Viewer (img)
- Nucleome browser (github at https://github.com/nucleome) (img)
- Pileup.js (img)
- Trackster (img)
- UCSC genome browser (img)
- Valis browser (img)
- WashU epigenomics browser (features redesign, there is also a legacy version) (img)
- Zenbu (img)
- UTGB (University of Tokyo Genome Browser) (img)
- Argo (img)
- 10x genomics/Loupe (img)
- Alamut (img)
- ATCC Genome Portal (American Type Culture Collection) (img)
- Benchling (img)
- CLC Genomics workbench (img)
- DNASTAR (img)
- Geneious (img)
- Genestack (img)
- Golden Helix (img)
- Lucid viewer (img)
- MacVector (img)
- Persephone (img)
- SnapGene (img)
- Strand NGS (img)
- Bionano (img)
- Circa (img)
- ERGO (img)
- AA (alignment annotator) (also see STRAP) (img)
- abrowse (img)
- alignment.js (img)
- AlignmentComparator (Uses http://bioinfweb.info/LibrAlign/) (img)
- AlignmentViewer (img)
- AliView (img)
- BioJS/MSA (img)
- rMSA (Can automate boxshade) (img)
- Boxshade (Also available as a command line tool with
apt install boxshade
. See also rMSA which can automate running boxshade from within R) (img) - ESPript (img)
- Jalview (img)
- JSAV (img)
- MSABrowser (img)
- msaR (uses BioJS/MSA) (img)
- MView (img)
- NCBI MSA Viewer (img)
- pyBoxshade (also see boxshade) (img)
- pymsaplotter (img)
- React MSAViewer (img)
- react-msaview (img)
- seqotron (img)
- STRAP (also see AA) (img)
- TeXShade (img)
- Wasabi (img)
- SNIPViz (img)
- ALVIS (MSA viewer) (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)
- alignfigR (img)
- alen (img)
- ProViz (See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage) (img)
- MEGA-X (original paper from 1994 but actively updated. requires EULA for download) (img)
- AliTreeViz (img)
- ete (img)
- ggtree (see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example) (img)
- seqvisr (img)
- Seaview (img)
- CIAlign (Has useful utility functions to clean gaps and trim MSAs) (img)
- ggmsa (See also ggtree) (img)
- CView (img)
- aCNVViewer (img)
- CNVkit (img)
- BAMScale (img)
- cnvCurator (img)
- GenomeSpy (img)
- GenomePaint (Not open source) (img)
- covviz (img)
- PURPLE (intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts) (img)
- bcftools cnv (img)
- mocha (Has a full analysis pipeline associated with end result visualizations) (img)
- genevisR (img)
- copynumber (img)
- SnoopCGH (img)
- Genovar (img)
- CNANorm (img)
- Orchestral (img)
- CNSpector (img)
- sequenza (also see https://sequenzatools.bitbucket.io/#/home) (img)
- BAMSnap (img)
- ChIA-Pipe (img)
- CNView (img)
- CNVPlot (img)
- CNVpytor (img)
- DNAPlotLib (img)
- ExonIntron (img)
- FeatureViewer (img)
- Geneviz (img)
- Genome STRiP (img)
- GenomeTools (img)
- GenomeView (img)
- genoPlotR (img)
- ggbio (img)
- GGgenes (img)
- GGsashimi (img)
- gtrellis (img)
- Gviz (img)
- Hagfish (img)
- HiCPlotter (img)
- JVarKit/BamToSVG (img)
- Lollipops (img)
- Mason (img)
- Methplotlib (img)
- Pairoscope (img)
- pauvre (img)
- pyGenomeTracks (img)
- RACER (img)
- RepViz (img)
- Samplot (img)
- SashimiPlot (img)
- shabam (img)
- SparK (img)
- Spliceclust (img)
- Sushi (img)
- svist4get (img)
- svv (img)
- svviz (img)
- svviz2 (img)
- trackViewer (img)
- mummer2circos (img)
- cgplot (img)
- bcftools roh (Plots runs of homozygosity, has interactive plot-roh.py helper too) (img)
- Chimeraviz (img)
- clinker (gene fusion software) (img)
- arriba (img)
- FusionInspector (Uses igv.js) (img)
- MAVIS (img)
- GenomeView (java app) (img)
- pyBamView (See supplementary info for more figures, supports padded SAM/BAM which is fairly rare) (img)
- Chromatic (img)
- Gambit (img)
- LookSeq (img)
- udon (Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo) (img)
- GSSPlayground (img)
- Aequatus (img)
- AliTV (img)
- Artemis comparison tool (ACT) (img)
- Biodalliance comparative demo (img)
- Chromatiblock (img)
- CMap (img)
- CoGe (img)
- Comparative assembly hub / "snake track" (img)
- CrossBrowse (img)
- CVit (img)
- Cvit.js (img)
- EasyFig (img)
- GBrowse_syn (img)
- Genome Context Viewer (img)
- Genome-plots-processing (img)
- Genomicus (img)
- gggenomes (img)
- GIVE (img)
- mauve-viewer (img)
- MCScan (python version) (img)
- MCScanX (img)
- mGSV (multiple genome synteny viewer) (img)
- MizBee (img)
- Multiple genome viewer (img)
- OMA local synteny browser (img)
- pafr (img)
- Parasight (Examples at https://ratparalogy.gs.washington.edu/) (img)
- progressiveMauve viewer (img)
- SyMap (img)
- Synima (img)
- Synteny browser (img)
- SynTView (img)
- SynVisio (img)
- Tripal MapViewer (img)
- VISTA browser (img)
- XMatchView (img)
- LinearDisplay.pl (readme says to cite this paper) (img)
- FastANI (img)
- clinker (img)
- RectChr (img)
- pretzel (img)
- PipMaker (See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html) (img)
- WGDI (img)
- BRIG (img)
- GENESPACE (img)
- miropeats (image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf) (img)
- syntenyPlotteR (img)
- chromoMap (img)
- SafFire (img)
- SimpleSynteny (img)
- Cinteny (img)
- AutoGraph (img)
- EvolutionHighway (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)
- Smash++ (img)
- plotsr (Blurs the line between synteny and SV visualization, a good thing!) (img)
- GenomeMatcher (img)
- SynBrowse (img)
- Sybil (Download https://sourceforge.net/projects/sybil/) (img)
- SyntenyPortal (img)
- CHROMEISTER (img)
- r2cat (img)
- SequenceSurveyor (img)
- BactoGENIE (img)
- PSAT (img)
- TreeBrowser (MicrobesOnline) (img)
- Combo (Based on the tool 'Argo') (img)
- GenomicBreaks (img)
- GenomeSyn (img)
- CrowsNest (img)
- GGisy (img)
- multiGenomicContext (img)
- AccuSyn (img)
- PureScript genetics browser (img)
- Locuszoom (Also see locuszoom.js http://locuszoom.org/locuszoomjs.php) (img)
- LDBlockShow (img)
- ggplot2 manhattan plot (This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2) (img)
- CMPlot (img)
- GeneticsMakie.jl (img)
- shinyChromosome (img)
- D-GENIES (img)
- Delly-maze (see also https://www.gear-genomics.com/maze/) (img)
- Discoplot (img)
- Dot (Python data preparation script) (img)
- Dotlet (The original publication was 2000 but updated ~2020 with reactjs) (img)
- Dotplot (chirimoyo)
- iLambda/Dotplot
- dotPlotly (img)
- Dottup (also seen here http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf) (img)
- FlexiDot (img)
- Gepard (img)
- Jdot (img)
- last-dotplot (img)
- mcutils (https://twitter.com/mjpchaisson/status/1040363992206569472) (img)
- Minidot (img)
- Mummer-idotplot
- Mummerplot (img)
- ggplot2 mummerplot (img)
- Redotable (img)
- syntenyPlotByR (img)
- Dotter (img)
- JGI/IMG (Dotplot use MUMmer) (img)
- MashMap (img)
- oxford-plots (Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt) (img)
- DAGchainer (img)
- 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)
- AGB assembly graph browser
- Bandage (See also BandageNG https://github.com/asl/BandageNG) (img)
- gfaestus (See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4) (img)
- graphgenomeviewer (img)
- MoMi-G (img)
- odgi draw + odgi viz + odgi inject (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)
- sequence tube map (img)
- Shasta (Uses graphviz) (img)
- LINX (part of the PURPLE/GRIDSS/LINX pipeline) (img)
- GfaViz (img)
- panGraphViewer (img)
- IGGE (Not open source) (img)
- gGnomes (img)
- gGnomes.js (img)
- Ribbon (img)
- Gremlin (img)
- InGAP-SV (img)
- Introgression browser (img)
- SplitThreader (img)
- SMRT View (wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View) (img)
- asgart (img)
- NeoLoopFinder (img)
- SVPV (img)
- AmpliconArchitect (The term amplicon refers essentially to extrachromosomal DNA in cancer) (img)
- Alan (img)
- Alv (img)
- ASCIIGenome (img)
- Bamcov (img)
- BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)
- Hapviz (img)
- plotReads (img)
- Rna Alignment Viewers (Colorstock, SScolor, Ratón) (img)
- Sam2pairwise
- Samtools depth visualization (img)
- Samtools tview (img)
- SvABA (img)
- VizAln (from HipSTR) (img)
- Anvio
- BioCircos.js (img)
- Circleator (img)
- circlize (img)
- Circos (the github repo is not up to date with the latest code) (img)
- CircosJS (img)
- DNAPlotter (img)
- GenomeProjector (img)
- JupiterPlot (img)
- OGDRAW (img)
- Gview (img)
- RegulomeExplorer (img)
- CGView (See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/) (img)
- pyCircos (See also https://github.com/ponnhide/plasmidviewer) (img)
- Apollo (img)
- D3GB (img)
- DNASkittle (img)
- EaSeq (img)
- FluentDNA (img)
- Gnomad browser (img)
- Hawkeye (img)
- IslandViewer and IslandPlot (web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG) (img)
- MagicViewer (img)
- Panoptes (img)
- MapView (links in original paper are dead, but URL provided here works) (img)
- NGB (img)
- SeqCover (img)
- SEQing (img)
- SFARI (img)
- Short read assembly browser (img)
- SNPitty (img)
- Staden (img)
- TASUKE (info about multi-genome-browser https://tasuke.dna.affrc.go.jp/) (img)
- TE-nest (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)
- Transposcope (img)
- UGENE (img)
- Varsome (img)
- Vials
- wasm bigwig demo browser (img)
- GWAS catalog browser (img)
- Human genome dating (made with vega/d3) (img)
- PopSV (img)
- SWAV (img)
- Haploview (img)
- Chip Monk (Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) (img)
- Chipster (Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf) (img)
- cisGenome Browser (img)
- Epilogos (img)
- Epiviz (img)
- HiPiler (img)
- Juicebox (img)
- Juicebox.js (img)
- Peax (img)
- CoolBox (fork of pyGenomeTracks) (img)
- eweitz/Ideogram (img)
- Ideogram (img)
- Ideoplot
- karyoploteR (img)
- KaryotypeSVG (img)
- NCBI Genome Decoration (img)
- UCSC Genome Graphs (img)
- genomegraphs (img)
- IdeoViz (img)
- Flash Gviewer (img)
- Ideogram viewer (img)
- chromPlot (img)
- PhenoGram (Can be web server or download) (img)
- RIdeogram (img)
- Pan-Tetris (img)
- Panacaea (img)
- Panache (img)
- panX (img)
- RPAN (3kricedb) (img)
- PGAP-X (img)
- PGV (img)
- Phandango (img)
- Protael (img)
- ProteinPaint (Not open source) (img)
- pViz (img)
- Aquaria (img)
- nightingale/protvista (Used on InterProScan website https://www.ebi.ac.uk/interpro/) (img)
- drawProteins (img)
- IBS (Illustrator for Biological Sequences) (img)
- PFAM generate_graphic (Also see guide here https://pfam.xfam.org/help#tabview=tab10) (img)
- Prosite/MyDomains (img)
- REPAVER (img)
- GraphAlignmentViewer (img)
- REViewer (See also GraphAlignmentViewer, similar look and from illumina also) (img)
- StainedGlass (img)
- ALVIS (chimeric alignment viewer) (img)
- vcfR (image shows chromoqc output) (img)
- NanoMethViz (img)
- AnnoJ (See list of instances of the browser here https://ecker.salk.edu/genome-browser/) (img)
- modbamtools (img)
- vega (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)
- MIRA (orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf) (img)
- wiggleplotr (img)
- Trackplot (suggests citing bwtool linked here) (img)
- Awesome Bioinformatics
- Genocat large collection of genomic visualizations with great review paper accompaniment https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727
- awesome-biological-visualizations
Send in PRs for more stuff!
This README.md and TOOLS.json are CC0 https://creativecommons.org/publicdomain/zero/1.0/
The website code is MIT