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 (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 (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)
• Zenbu (img)
• UTGB (University of Tokyo Genome Browser) (img)
• Argo (img)
• ABrowse (genome browser) (Had integrations with BioMart, Taverna) (img)
• gtracks (Powered by pyGenomeTracks) (img)
• trackplot (python) (img)

Commercial

• 10x genomics/Loupe (img)
• Alamut (img)
• ATCC Genome Portal (img)
• Benchling (img)
• CLC Genomics workbench (img)
• DNASTAR (img)
• Geneious (img)
• Genestack (img)
• Golden Helix (Free for academic use) (img)
• Lucid viewer (img)
• MacVector (img)
• Persephone (img)
• SnapGene (img)
• Strand NGS (img)
• Bionano (img)
• Circa (img)
• ERGO (img)

MSA

• AA (alignment annotator) (also see STRAP) (img)
• abrowse (MSA viewer) (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 (Primarily a web interface but can download a binary for linux https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php) (img)
• Jalview (img)
• JSAV (img)
• MSABrowser (img)
• msaR (uses BioJS/MSA) (img)
• MView (See also their web versions of clustal omega etc. which have similar outputs) (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)

Logo

• LogoJS (img)

CNV

• aCNVViewer (img)
• CNVkit (img)
• BAMScale (img)
• cnvCurator (img)
• GenomeSpy (img)
• SFARI (img)
• SNPitty (img)
• GenomePaint (Demos https://proteinpaint.stjude.org/bam/) (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)
• CoveragePlotter (See also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for multi-chromosome) (img)
• genome_coverage_plotter (img)
• SeeNV (img)

Static

• 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 (See also https://pypi.org/project/gtracks/ which is a separate project that is powered by pyGenomeTracks) (img)
• RACER (img)
• RepViz (img)
• Samplot (img)
• SashimiPlot (See also rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of Transcript Splicing) (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)
• geneviewer (img)

Gene fusion

• Chimeraviz (img)
• clinker (gene fusion software) (img)
• arriba (img)
• FusionInspector (Uses igv.js) (img)
• MAVIS (img)

Alignments viewer

• GenomeView (java app) (img)
• pyBamView (See supplementary info for more figures, supports padded SAM/BAM which is fairly rare) (img)
• Chromatic (img)
• Gambit (img)
• Hawkeye (img)
• LookSeq (img)
• MapView (links in original paper are dead, but URL provided here works) (img)
• NGB (img)
• Short read assembly browser (img)
• Staden (img)
• udon (Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo) (img)
• wally (img)
• alignoth (img)
• gw (img)
• DrukBam (img)
• bamscope (img)

Comparative

• 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 (Includes a powerful analysis pipeline, worth reading the paper) (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 (see also https://github.com/schneebergerlab/syri) (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)
• pyGenomeViz (See also https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz https://github.com/moshi4/plot_genome_align_fig) (img)
• ShinySyn (img)
• NCBI CGV (img)
• asynt (img)
• NGenomeSyn (See also RectChr) (img)
• chromsyn (img)
• syntR (img)
• GCSnap (img)
• ModDotPlot (img)
• odp (oxford dot plots) (Pub is not for visualization tool, but it is suggested to cite this paper) (img)
• ntSynt (Uses gggenomes) (img)
• SYNY (img)

Single cell

• Millefy (img)
• gingko (img)
• copykat (img)
• scCNV_heatmap (img)
• casper (img)
• ArchR (img)
• numbat (img)
• MosaicCatcher pipeline (img)

GWAS

• PureScript genetics browser (img)
• Locuszoom (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)

Dotplot

• 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)

Gene structure

• TnT (img)
• Apollo aka WebApollo (img)
• D3GB (Live link http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963 doesn't work anymore) (img)
• ggtranscript (img)

Microbiology

• Edinburgh-Genome-Foundry/DnaFeaturesViewer (See also https://github.com/Edinburgh-Genome-Foundry/Caravagene) (img)
• IslandViewer and IslandPlot (web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG) (img)
• GeneViTo (img)
• GECO (img)
• GeCoViz (img)
• clonifier (img)

Graph

• AGB assembly graph browser (img)
• 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)
• ctag (See also hygene https://github.com/ProgrammingLife2017/hygene) (img)
• PGR-TK (img)
• VRPG (img)
• SGTK (scaffold graph toolkit) (img)
• pgv (graph tool) (img)
• VAG (img)
• waragraph (Deployed to the web via wasm) (img)

SV

• 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)
• bigly (img)
• vcf2circos (Based on PCircos https://github.com/CJinny/PCircos) (img)
• ReConPlot (img)
• SVhawkeye (img)

Text based

• 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)
• pileuppy (img)
• rich-msa (img)

Circular

• Anvio
• BioCircos.js (img)
• Circleator (img)
• circlize (img)
• Circos (no official github to my knowledge) (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)
• pyCirclize (img)
• OmicCircos (img)
• genoVi (img)
• BRICK (BRIG-like circular knowledgebase) (See also BRIG) (img)

Synthetic biology

• seqviz (img)
• ApE (a plasmid editor) (img)
• Chopchop (img)
• plasmapR (img)

Historical

• Apollo (URL is an archive.org link) (img)
• Internet Contig Explorer (img)

Exotic

• DNASkittle (img)
• FluentDNA (img)
• BigTop (img)
• Cylindrical alignment app (img)
• sockeye (img)
• spinteny (img)

Epigenomics

• EaSeq (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)
• JBR (Not open source, at least not on github) (img)
• python-genome-browser aka pygbrowse (img)

Linear

• Gnomad browser (img)

Expression

• GTEX Locus browser (img)

Population

• GWAS catalog browser (img)
• Human genome dating (made with vega/d3) (img)
• Panoptes (img)
• PopSV (img)
• vcfR (image shows chromoqc output) (img)
• SWAV (img)
• Haploview (img)
• pixy (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)

Assembly QC

• Icarus QUAST (img)
• ALVIS (chimeric alignment viewer) (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)

Alignment viewer

• MagicViewer (img)

Uncategorized

• Locuszoom.js

Coverage

• SeqCover (img)
• wiggleplotr (img)
• Trackplot (R) (img)
• signac (img)
• ggcoverage (img)
• BAMdash (img)

Special-purpose

• SEQing (img)
• UGENE (img)

Pangenome

• TASUKE (info about multi-genome-browser https://tasuke.dna.affrc.go.jp/) (img)
• Pan-Tetris (img)
• Panacaea (img)
• Panache (img)
• panX (img)
• RPAN (3kricedb) (img)
• PGAP-X (img)
• PGV (pangenome tool) (img)
• Phandango (img)

Transposons

• 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/. the github link is re-hosted source code also downloaded from archive.org) (img)
• Transposcope (img)

Annotation

• Varsome (img)

Splicing

• Vials
• splicejam (img)
• Slinker (See also, clinker (gene fusion software)) (img)

Quantitative

• wasm bigwig demo browser (img)

Ideogram

• eweitz/Ideogram (img)
• Ideogram (img)
• Ideoplot
• karyoploteR (img)
• KaryotypeSVG (img)
• NCBI Genome Decoration (Was located at https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023) (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)
• tagore (img)
• ezcharts (img)
• chrov (See also usage in https://github.com/rraadd88/beditor) (img)

Mobile app

• iGenomics (img)

Protein

• Protael (img)
• ProteinPaint (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)
• TogoStanza Protein Browser (img)

Heatmap

• UCSC Xena (img)
• VIVA (img)

Repeats

• REPAVER (img)
• GraphAlignmentViewer (img)
• REViewer (See also GraphAlignmentViewer, similar look and from illumina also) (img)
• StainedGlass (img)
• SODA (Describes itself as a low-level library to create larger applications with) (img)
• TRVZ (TRGT tandem repeat genotyping visualizer) (img)

Methylation

• NanoMethViz (img)
• AnnoJ (See list of instances of the browser here https://ecker.salk.edu/genome-browser/) (img)
• modbamtools (img)

Phylogenetics

• Nextclade (Related usage on nextstrain app also) (img)
• Gingr (img)
• Taxonium (Genome variation visualisation in Taxonium is provided by the 'Treenome Viewer': https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450) (img)

Long reads

• methylartist (img)

Hi-C

• Plotgardener (img)
• gcMapExplorer (img)
• PretextView (img)
• figeno (img)

Deadlink

• VAMP (img)
• CGH-Explorer (img)
• DNAVis (img)

BLAST

• SequenceServer (img)

Academic license

• Consed (img)

Local ancestry

• fineSTRUCTURE aka ChromoPainter (img)
• MOSAIC (img)

Variation

• snpit (img)
• vcfPlotein (img)
• NucFreq (img)

Chromosome painting

• GeMo (img)

K-mer

• Panagram (img)

Other lists

• 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!

License

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

The website code is MIT