346个基因组可视化工具一网打进！

已于 2024-04-22 16:24:17 修改
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文章标签： 生物信息工具 生信宝典
于 2021-11-04 22:13:00 首次发布
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Github来源：https://github.com/cmdcolin/awesome-genome-visualization

配套网页：

https://cmdcolin.github.io/awesome-genome-visualization/?latest=true

工具名称、下载链接、文献、编程语言、运行平台如下

Ideogram viewer

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‍

https://bioinformatics.mdanderson.org/public-software/ideogramviewer/

Language: JS

‍‍

Platform: Web

‍

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BRIG

http://brig.sourceforge.net

Publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402

Language: Java

Tags: Comparative, Circular

Platform: Desktop

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GenomeMaps

http://www.genomemaps.org/

Publication: https://academic.oup.com/nar/article/41/W1/W41/1113984

Language: JS

Tags: General, Deadlink

385e0b04d7c639fb634abcb257d1806c.png

gcMapExplorer

https://github.com/rjdkmr/gcMapExplorer

Language: Python

Tags: Hi-C

754862c8964449e2df53d23ce25eef86.png

Trackplot

https://github.com/PoisonAlien/trackplot

Language: R

Tags: Coverage, Gene structure

afd7175a1dcb829bd914549f80324ad4.png

REViewer

https://github.com/Illumina/REViewer

Publication: https://www.biorxiv.org/content/10.1101/2021.10.20.465046v1.full.pdf

Tags: Repeats

Note: See also GraphAlignmentViewer, similar look and from illumina also

6f36850555f0f4427fbfc4ce3e360240.png

PGV

https://github.com/ucrbioinfo/PGV

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04424-w

Language: Python

Tags: Pangenome, Dotplot, Comparative

Platform: Web

d400505a21a9eb95064d9cad1a8597cd.png

AmpliconArchitect

https://github.com/virajbdeshpande/AmpliconArchitect

Language: Python

Tags: SV, Cancer

Note: The term amplicon refers essentially to extrachromosomal DNA in cancer

e8850862f0cdc84b7fea3b7925576766.png

WGDI

https://github.com/SunPengChuan/wgdi

Publication: https://www.biorxiv.org/content/10.1101/2021.04.29.441969v1.full.pdf

Language: Python

Tags: Comparative, Dotplot, Circular

b768fe51ea6b7a4aaf16ba7483c2748b.png

AliTreeViz

https://www.npmjs.com/package/alitreeviz

Language: JS

Tags: MSA, Phylogenetics

168339908fedb47b9e27cde40f235e70.png

Haploview

https://www.broadinstitute.org/haploview/haploview

Language: Java

Platform: Desktop

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MEGA-X

https://www.megasoftware.net/

Tags: MSA, Phylogenetics

Platform: Desktop

55d96743d63b6c3fe788741a51f8f759.png

GraphAlignmentViewer

https://github.com/Illumina/GraphAlignmentViewer

Tags: Repeats

865f4567d22a439ceb45b737a7d569a7.png

PipMaker

http://pipmaker.bx.psu.edu/pipmaker/

Tags: Comparative, Repeat, Annotation

Note: See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html

84662a64205e88d93caa13d54c6469e6.png

IGGE

https://github.com/immersivegraphgenomeexplorer/IGGE

Publication: https://www.researchgate.net/profile/Aviv-Elor/publication/354582953_The_Immersive_Graph_Genome_Explorer_Navigating_Genomics_in_Immersive_Virtual_Reality/links/6140c890578238365b0afa3a/The-Immersive-Graph-Genome-Explorer-Navigating-Genomics-in-Immersive-Virtual-Reality.pdf

Tags: Graph, Exotic

Note: Not open source

8dd270499dc81293d4c005a5c3d1dac9.png

oxford-plots

https://github.com/jherrero/oxford-plots

Language: R, Perl

Tags: Dotplot

Note: Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt

c6ff09caddf7079aa1c1fe16c5eb804e.png

MIRA

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Publication: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf

Language: C++

Tags: Assembly, Alignment viewer, Historical

48507f7b2f455c6e557b12844594e02e.png

Plotgardener

https://github.com/PhanstielLab/plotgardener/

Publication: https://www.biorxiv.org/content/10.1101/2021.09.08.459338v1

Language: R

Tags: Hi-C, Coverage

2968aba7a9885ce509b0210cfa2cec54.png

Flash Gviewer

http://gmod.org/wiki/Flashgviewer/

Language: Flash, ActionScript

Tags: Ideogram, Genetic Map, Historical

9c80a7b85be4f1ed3b7319e621c462dd.png

IdeoViz

https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf

Language: R

Tags: Ideogram, Quantitative, Splicing

18b2895b3b20ee177b070000d2e32d5c.png

genomegraphs

http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf

Language: R

Tags: Ideogram, Quantitative, Splicing

8e6e33f1bce09ac2913d54ecaaa57e10.png

splicejam

https://github.com/jmw86069/splicejam

Language: R

Tags: Splicing, Sashimi

feee18bd9ba1448fbafaec9086c6ae20.png

pretzel

https://github.com/plantinformatics/pretzel

Language: JS, D3

Tags: Comparative, Genetic map

1a8495e52275d09b88e48461acb939ba.png

wiggleplotr

http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html

Language: R

Tags: Coverage

cb5cd7d21b724ea180dcf5bfbe239bd6.png

SVPV

https://github.com/VCCRI/SVPV

Publication: https://academic.oup.com/bioinformatics/article/33/13/2032/3056003

Language: Python

Tags: SV, Coverage

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panGraphViewer

https://github.com/TF-Chan-Lab/panGraphViewer

Language: Python

Tags: Graph, Pangenome

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ProViz

http://slim.icr.ac.uk/proviz/index.php

Publication: https://academic.oup.com/nar/article/44/W1/W11/2499309

Language: JS

Tags: MSA, Protein

Note: See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage

81a2d1b9bbdcca6d0e3514d690c01ef9.png

MAVIS

http://mavis.bcgsc.ca/

Language: Python

Tags: Gene fusion, SV

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PGAP-X

https://pgapx.zhaopage.com/

Publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4337-7

Language: C++

Tags: Pangenome

Platform: Desktop

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ArchR

https://www.archrproject.com/articles/Articles/tutorial.html

Language: R

Tags: Single cell

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nightingale/protvista

https://ebi-webcomponents.github.io/nightingale/#/msa

Tags: Protein, MSA

Platform: Web

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vega

http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL

Tags: Assembly, Historical, Genetic map

Note: Mentioned in https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf

Platform: Web

f69e30e9b150c1e8e31d6ec781a28c0c.png

Aquaria

http://aquaria.ws/Q9HD67/5i0i/A

Tags: Protein, MSA

Platform: Web

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alen

https://github.com/jakobnissen/alen

Language: Rust

Tags: MSA, Text based

5d819f16f845f37bb0ee3a0e63077ee1.png

NeoLoopFinder

https://github.com/XiaoTaoWang/NeoLoopFinder

Language: Python

Tags: SV, Hi-C

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FusionInspector

https://github.com/FusionInspector/FusionInspector/wiki

Language: Perl, JS

Tags: Gene fusion

Note: Uses igv.js

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arriba

https://github.com/suhrig/arriba

Publication: https://genome.cshlp.org/content/31/3/448

Language: C++, R

Tags: Gene fusion

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clinker (gene fusion)

https://github.com/Oshlack/Clinker/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6065480/

Language: R

Tags: Gene fusion

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LDBlockShow

https://github.com/BGI-shenzhen/LDBlockShow

Publication: https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbaa227/5939575?redirectedFrom=fulltext

Language: C++, Perl

Tags: GWAS, Population

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RectChr

https://github.com/BGI-shenzhen/RectChr

Tags: Comparative, Ideogram, Static

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casper

https://github.com/akdess/CaSpER

Publication: https://www.nature.com/articles/s41467-019-13779-x

Language: R

Tags: Single cell, CNV

cb35326b4b7f520e47cd58f5e528e4a6.png

scCNV_heatmap

https://github.com/StefanKurtenbach/scCNV_heatmap

Language: Python

Tags: Single cell, CNV

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copykat

https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf

Language: R

Tags: Single cell, CNV

8384c739aa4125e0723d15ef32bb388e.png

alignfigR

https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html

Language: R

Tags: MSA

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copynumber

https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf

Language: R

Tags: CNV

bd409e7bdaa3b5a610d6a784453ef22b.png

SWAV

http://swav.popgenetics.net/

Publication: https://www.nature.com/articles/s41598-019-57038-x

Tags: Population, Deadlink

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methylartist

https://github.com/adamewing/methylartist

Language: Python

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AnnoJ

https://brainome.ucsd.edu/howto_annoj.html

Language: JS

Tags: Methylation

Note: See list of instances of the browser here https://ecker.salk.edu/genome-browser/

Github: https://github.com/mukamel-lab/annoj_cndd

Platform: Web

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udon

https://github.com/ocxtal/udon

Language: Rust

Tags: Alignment viewer

Note: Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo

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MashMap

https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot

Tags: Dotplot

e20584b2c76ec67b9ad74bcfc8021350.png

asgart

https://github.com/delehef/asgart

Publication: https://academic.oup.com/bioinformatics/article/34/16/2708/4948616

Language: Rust

Tags: SV, Ideogram, Circular, Linear

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vcfR

https://knausb.github.io/vcfR_documentation/

Language: R

Tags: QC, Population, Coverage

Note: image shows chromoqc output

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Nextclade

https://clades.nextstrain.org/

Language: JS, React, D3

Tags: Phylogenetics

Note: Related usage on nextstrain app also

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GfaViz

Publication: https://academic.oup.com/bioinformatics/article/35/16/2853/5267826

Language: C++

Tags: Graph

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NanoMethViz

http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html

Publication: https://www.biorxiv.org/content/10.1101/2021.01.18.426757v3

Language: R

Tags: Methylation

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genevisR

https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html

Language: R

Tags: CNV

2e8a3d9ce522749b9f8e5a6ec7ff816e.png

ALVIS (chimeric alignment viewer)

https://github.com/SR-Martin/alvis

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Tags: QC, Assembly

18ff205e440a4f8dfcbba2e0a1dbdfed.png

ALVIS (MSA viewer)

https://www.ebi.ac.uk/research/goldman/software/alvis

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856975/

Tags: MSA

Note: Introduces sequence bundles concept, also see web app version https://www.ebi.ac.uk/goldman-srv/sequencebundles/

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mocha

https://github.com/freeseek/mocha#plot-results

Language: C, WDL, R

Tags: CNV

Note: Has a full analysis pipeline associated with end result visualizations

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bctools cnv

https://samtools.github.io/bcftools/howtos/cnv-calling.html

Tags: CNV

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bcftools roh

https://samtools.github.io/bcftools/howtos/roh-calling.html

Language: Python

Tags: Static

Note: Plots runs of homozygosity, has interactive plot-roh.py helper too

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Internet Contig Explorer

https://www.bcgsc.ca/resources/software/ice

Publication: https://genome.cshlp.org/content/13/6a/1244.long

Tags: Historical

fcb56674befa823a4f6603affb1aa034.png

spinteny

https://github.com/skinner/spinteny

Tags: Exotic, Comparative

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sockeye

https://www.bcgsc.ca/resources/software/sockeye

Publication: https://genome.cshlp.org/content/14/5/956.full

Tags: Exotic, Comparative

f8d10acc8b18a641c91769792fdd868a.png

SMRT View

http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm

Tags: SV

Github: https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View

4fe9ed85cd4428acffef296e1fe7e409.png

PURPLE

https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md

Tags: CNV, Cancer

Note: intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts

e4dd63c58870036acc55285353d0f308.png

LINX

https://github.com/hartwigmedical/hmftools/blob/master/sv-linx/README_VIS.md

Tags: Graph, SV, Breakends, Circular, Linear, Gene fusion, Cancer

Note: part of the PURPLE/GRIDSS/LINX pipeline

531ef9511543290c04d284a4886d2e0b.png

Shasta

https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph

Language: C++

Tags: Graph

Note: Uses graphviz

Platform: Web, Localhost, CLI

48665d1eed1a5344f9aa6ee245c9c4f4.png

PopSV

https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md

Language: R

Tags: Population, SV

Platform: Web

806abe2902d81a680f616078b458402b.png

clinker

https://github.com/gamcil/clinker

Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab007/6103786

Language: JS

Tags: Comparative, Gene order

Platform: Web

fadab709bf6b3d6f2f8590dc4f85c715.png

covviz

https://brwnj.github.io/covviz/

Language: JS

Tags: CNV, Coverage, Population

dce44cb6eead174e09a4a680f5772599.png

JGI/IMG

https://img.jgi.doe.gov/

Tags: Dotplot, Linear, Microbiology

Note: Dotplot use MUMmer

Platform: Web, Silo

bf71b4e4d5b199c680d19d70306950a6.png

FastANI

https://github.com/ParBLiSS/FastANI

Language: C++

Tags: Comparative, Microbiology

e65634c244ce036d0ea860a0aa12d6ff.png

Gview

https://server.gview.ca/examples

Tags: Circular, Linear, Pangenome, Microbiology

Platform: Web

d5a82d53be34a7baa04f3273a0003023.png

LinearDisplay.pl

https://github.com/JCVenterInstitute/LinearDisplay

Language: Perl

Tags: Comparative

Platform: CLI

0e70eb6210c310887dcd677a218092c4.png

REPAVER

https://gitlab.com/gringer/bioinfscripts/

Publication: https://www.researchgate.net/publication/346507956_REPAVER_Paving_the_Way_for_Repeat_Discovery_in_Complex_Genomes?channel=doi&linkId=5fc58ba4a6fdcce95268fe60&showFulltext=true

Language: R, C++

Tags: Repeats, Dotplot, Static, Linear

Platform: CLI

494606a0af36165b03fcef683ef0f5b1.png

Dotter

https://sonnhammer.sbc.su.se/Dotter.html

Publication: https://pubmed.ncbi.nlm.nih.gov/8566757/

Tags: Dotplot

Platform: CLI

31525d805f4883ed0d20b2758f07f211.png

VIVA

https://www.biorxiv.org/content/10.1101/589879v1.full.pdf

Tags: Heatmap, Population, Variants

Platform: Web

d45a940ca368c683946816ac11fbd0cd.png

UCSC Xena

https://xena.ucsc.edu/

Tags: Heatmap, Population

Platform: Web

3a8270eac6c2eaab2f80b9ffbeef9303.png

pViz

https://github.com/Genentech/pviz

Tags: Protein

Platform: Web

1e4824b04c4a92efd45a4fd45bd1e608.png

GenomePaint

https://genomepaint.stjude.cloud/

Publication: https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30659-0

Tags: CNV, Linear, Cancer, Lollipops

Note: See also gallery here https://genomepaint.stjude.cloud/#figures

Platform: Web

190a832631f50a0312d86be5e0ce084a.png

ProteinPaint

https://pecan.stjude.cloud/proteinpaint

Publication: https://www.nature.com/articles/ng.3466

Tags: Protein, Cancer, Lollipops

Platform: Web

e9548e241760041cad00779b67e3ac1e.png

Protael

http://sanshu.github.io/protaelweb/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963358/

Language: JS

Tags: Protein, MSA

Platform: Web

df8e90da8d4558f82dbcbf23d67dceaa.png

RPAN (3kricedb)

http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF

Tags: Pangenome, JBrowse integration

Platform: Web

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Panache

https://github.com/SouthGreenPlatform/panache

Tags: Pangenome

7edadf8cf3b5e3cfaf78a35abefe338e.png

Panacaea

https://github.com/JCVenterInstitute/PanACEA

Tags: Pangenome

878ce97ebba8daef9ef6f89aaa630ef5.png

Pan-Tetris

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/

Tags: Pangenome

61d9a2457208c91095c544eaf97575ce.png

iGenomics

https://www.biorxiv.org/content/10.1101/2020.02.11.944132v1

Tags: Mobile

a512a14a10f9dd124670706cfc1bfa47.png

UCSC Genome Graphs

http://genome.ucsc.edu/cgi-bin/hgGenome

Tags: Ideogram

Platform: Web, Form, Silo

cfbf98a488c725da92b994bcd0face37.png

NCBI Genome Decoration

https://www.ncbi.nlm.nih.gov/genome/tools/gdp/

Tags: Ideogram

Platform: Web, Form, Silo

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KaryotypeSVG

https://github.com/andreasprlic/karyotypeSVG

Language: JS, SVG

Tags: Ideogram

Platform: Web

9d99751be1d7a06d96987780a6f6cf30.png

karyoploteR

https://github.com/bernatgel/karyoploteR

Language: R

Tags: Ideogram, Static

e9ef2e18d0acbb2db5d0092e5d88e066.png

Ideogram

https://github.com/RCollins13/HumanIdiogramLibrary

Language: SVG

Tags: Ideogram, Static

5a98a9f60e9e0d796c8a778446629261.png

eweitz/Ideogram

https://github.com/eweitz/ideogram

Language: JS

Tags: Ideogram

Platform: Web

6d173cc917e4ad5357607109bc100256.png

chromoMap

https://www.biorxiv.org/content/10.1101/605600v1.full.pdf

Language: R

Tags: Ideogram, Static

54820464867916fa8fc7dcd2b046bf29.png

Peax

https://github.com/Novartis/peax

Language: JS

Tags: Epigenomics, Higlass integration

Platform: Web

af02e6113f0ab2dcbd49c0d851539071.png

Juicebox.js

http://www.igv.org/doc/juiceboxjs.html

Publication: https://www.cell.com/fulltext/S2405-4712(18)30001-2

Language: JS

Tags: Epigenomics, Hi-C

Platform: Web

c76150e8511319d7e1f80ee14f091d90.png

Juicebox

https://github.com/aidenlab/Juicebox

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596920/

Language: Java

Tags: Epigenomics, Hi-C

Platform: Desktop

e277c286087ba66963d694ac80704c1e.png

HiPiler

http://hipiler.higlass.io

Tags: Epigenomics, Hi-C, Higlass integration

Platform: Web

a4e2c8dd8900bb68bbcc56c4ec0544f2.png

Epiviz

https://epiviz.github.io/

Publication: https://www.biorxiv.org/content/10.1101/865295v1.full.pdf

Language: JS, R, D3

Tags: Epigenomics

Platform: Web

fb29c8f450c02dc21ea3a7499c44bfc7.png

Epilogos

https://epilogos.altius.org/

Tags: Epigenomics, Higlass integration

Platform: Web

15045aca4f487f468b8fd343a68a7f3a.png

cisGenome Browser

https://jhui2014.github.io/browser/screenshots.html

Language: C

Tags: Epigenomics

Platform: Desktop

820b24c0429fc1f6eeb03c4e1305be05.png

Chipster

https://chipster.csc.fi/

Language: Java

Tags: Epigenomics, CNV

Note: Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf

Platform: Desktop

0716dcd83297cd8b2424ca0798479cfe.png

Chip Monk

http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

Language: Java

Tags: Epigenomics

Note: Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Platform: Desktop

40b624ae63c4f740f626d6ae63e80bf3.png

syntenyPlotByR

https://github.com/shingocat/syntenyPlotByR

Language: R

Tags: Dotplot, Static

4259f9713bdebc0d0d7b403a78faaa35.png

Redottable

https://github.com/s-andrews/redotable

Language: Java

Tags: Dotplot

Platform: Desktop

03dd6f9c4ec4d55d168880283f54cae2.png

ggplot2 mummerplot

https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/

Language: R

Tags: Dotplot

90677d5dca08d7235cb658aa1df4cc1e.png

Mummerplot

http://mummer.sourceforge.net/

Language: GNUPlot

Tags: Dotplot, Static

864afceeabf686721ef1b372b077b9fb.png

Minidot

https://github.com/thackl/minidot

Language: R

Tags: Dotplot, Static

b3695f7d228dc19ef6b3ad888d754696.png

last-dotplot

http://last.cbrc.jp/

Tags: Dotplot

Platform: CLI, Web-server

eac7108151260549e1c60d59ab06e3be.png

Jdot

https://github.com/LyonsLab/jdot

Language: JS

Tags: Dotplot

Platform: Web

808b87e33ecb1cb65d34170237ee69d8.png

FlexiDot

https://github.com/molbio-dresden/flexidot

Language: Python

Tags: Dotplot

Platform: CLI

3d0f1f7c29b47ea719e0aa73f096ade9.png

Dottup

https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup

Tags: Dotplot

Note: also seen here http://eichlerlab.gs.washington.edu/publications/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf

5339fdfc0217f5e9426f9fcbac5e8181.png

dotPlotly

https://github.com/tpoorten/dotPlotly/

Language: R, Shiny

Tags: Dotplot

Platform: Web

bfab9c73f6f5c94d14c3c819ba047e42.png

Dotlet

https://dotlet.vital-it.ch/

Language: JS

Tags: Dotplot

Platform: Web

7fcf39a13a8abb410d19906491e3c376.png

Dot

https://dot.sandbox.bio/

Tags: Dotplot

Github: https://github.com/MariaNattestad/dot

Platform: Web

a3ada8dae8ba1e26500635758e06da6f.png

Discoplot

https://github.com/mjsull/DiscoPlot

Language: Python

Tags: Dotplot, Static

6dab83827670f4c985071bb702e08795.png

Delly-maze

https://github.com/dellytools/maze

Language: Python

Tags: Dotplot, Static

910eebea79090020e9cf1bd8af9c7f4b.png

D-GENIES

http://dgenies.toulouse.inra.fr/

Language: JS, Python, D3

Tags: Dotplot

Github: https://github.com/genotoul-bioinfo/dgenies

Platform: Web

eb8f4dff4bbb74f471f33fbef89448e9.png

cgplot

https://github.com/dfguan/cgplot

Language: Python

Tags: Static, Dotplot

941b930f7362c2e943817be6a352e724.png

Zenbu

http://fantom.gsc.riken.jp/zenbu/

Tags: General

Platform: Web

e2c92edecd63227ff7a944238c12bd97.png

WashU epigenomics browser

https://epigenomegateway.wustl.edu/

Language: JS, React

Tags: General, Epigenomics, Hi-C

Platform: Web

2de296f4434d9e466b3e1ab173930f9b.png

Valis browser

https://valis.bio/

Language: JS, WebGL

Tags: General, Quantitative, Epigenomics

Platform: Web

ee272b200ee36be3d6fd4199f65ec9c9.png

UCSC genome browser

https://genome.ucsc.edu/

Tags: General

Platform: Web, Silo

5896b86a4723e296c58c74e50c3c0fa1.png

Trackster

https://galaxyproject.org/learn/visualization/

Tags: General

Platform: Web

eca8f33e9701ef5007bfdebdc1a215e1.png

Pileup.js

https://github.com/hammerlab/pileup.js/

Language: JS

Tags: General, SV

Platform: Web

987704cc9a6aea4e37072b3423dd6df3.png

Nucleome browser

https://vis.nucleome.org/v1/main.html

Language: JS

Tags: General, Multi

Platform: Web

fbc81141e6f5cbbbc13e2c83238ac61b.png

NCBI Genome Data Viewer

https://www.ncbi.nlm.nih.gov/genome/gdv/

Tags: General, SV, Epigenomics, Gene structure, Splicing

Platform: Web, Silo

a7941f30a88654ebffa3223322691dab.png

Kero-BROWSE

https://kero.hgc.jp/examples/CLCL/hg38/index.html

Language: JS

Tags: General, SV, Alignment viewer

Platform: Web

f5bb667745714ec4d2a4f90467cd79dd.png

JBrowse 2

http://jbrowse.org/jb2

Language: JS, Typescript, React

Tags: General, SV, Comparative, Dotplot, Circular, Alignment viewer, Quantitative, Hi-C

Note: See gallery for more examples https://jbrowse.org/jb2/gallery

Platform: Web

9aa959ee14702cbdf8b7778ae43e1558.png

JBrowse

http://jbrowse.org/jbrowse1.html

Language: JS

Tags: General, Alignment viewer, SV, Quantitative, Gene structure

Note: See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron

Platform: Web, Desktop

ad37e9c464d6242aa6ae73326aca0df6.png

IGV.js

https://github.com/igvteam/igv.js/

Tags: General, Alignment viewer

Platform: Web

70e8cb334fa565b8efdcdade34da3d74.png

HiGlass

https://higlass.io

Language: JS, WebGL

Tags: General, Epigenomics, Hi-C

Platform: Web

1f0a976be6601fb78ab6603c56292507.png

Gosling

https://gosling.js.org/

Language: JS, WebGL, Typescript, React

Tags: General, Epigenomics, Higlass integration, Linear, Circular, Comparative, Quantitative

Platform: Web

f6e6c29f03d271894f0152bce45ffbb4.png

GBrowse+GBrowse 2

http://gmod.org/wiki/GBrowse

Language: Perl

Tags: General

Platform: Web

207303348ed7a049ab9c98f59451ee23.png

Ensembl genome browser 2020 edition

http://2020.ensembl.org/

Tags: General, Comparative

Platform: Web

4a305c37e3b962b4fff4ef94dbb0f37c.png

Ensembl genome browser

https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237

Tags: General, Comparative

Platform: Web, Silo

f43f8aa76e1db055db6da6ca5502eca4.png

Biodalliance

http://www.biodalliance.org/

Language: JS

Tags: General, Alignment viewer

Platform: Web

46e934303408c41e0aa38412abcda0e8.png

Cylindrical alignment app

https://sourceforge.net/projects/cylindrical-alignment-app/

Alt url https://sourceforge.net/projects/cyl-viewer/

Tags: Exotic

Platform: Desktop

4deff4f99313ae1f6e3bb56435d61697.png

BigTop

https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/

Tags: Exotic, GWAS

Github: https://github.com/dnanexus/bigtop

Platform: Web

5d4c493bc7bf6f5c9d53740a7bccccf1.png

Savant

http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/

Publication: https://pubmed.ncbi.nlm.nih.gov/22638571/

Language: Java

Tags: General, SV, Alignment viewer

Platform: Desktop

b926ca8c0533b7441770b9377f0a311e.png

IGV

https://igv.org/

Language: Java

Tags: General, Alignment viewer, SV, Quantitative

Platform: Desktop

a0e9625af2ae4533df520b623f5399bd.png

IGB

https://bioviz.org/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937187/

Language: Java

Tags: General, Alignment viewer

Platform: Desktop

7613e400cff74ba10e3b6330c2bcaad9.png

BasePlayer

https://baseplayer.fi/

Publication: https://www.biorxiv.org/content/10.1101/126482v1.full

Language: Java

Tags: General

Platform: Desktop

b2e783ddafb77a02eb79e20e49999e57.png

wasm bigwig demo browser

https://shk656461.github.io/index.html

Language: WASM

Tags: Special-purpose, Quantitative

Platform: Web

e346a342c93b1f7d56c1e4ac705fcb33.png

Varsome

https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET

Tags: Special-purpose, Annotation

Platform: Web, Silo

9853a1c962ee178f21ad80fad8707fed.png

UGENE

http://ugene.net/

Tags: Special-purpose

Platform: Desktop

e9ff141eb243b0f43ad6d576be7932cb.png

Transposcope

https://academic.oup.com/bioinformatics/article-abstract/36/12/3877/5820971?redirectedFrom=fulltext

Language: JS

Tags: Special-purpose, Transposons

Platform: Web

032ae7a7c43b306f1df6118f34dfc070.png

TE-nest

https://pubmed.ncbi.nlm.nih.gov/18032588

Tags: Special-purpose, Transposons, Deadlink?

Note: download link unknown

01b28c0d0d304572498cb1a9d7686de4.png

TASUKE

https://ricegenome.dna.affrc.go.jp/

Tags: Special-purpose, Pangenome

Platform: Web

c6764e7fbfe34fb4d233a7235bcfec48.png

Staden

https://sourceforge.net/projects/staden/

Tags: Special-purpose, Alignment viewer

Platform: Desktop

c91e412b7ffeb5d7d1460b183662d4aa.png

SplitThreader

http://splitthreader.com/

Tags: SV, CNV

Github: https://github.com/MariaNattestad/SplitThreader

Platform: Web

55d65a7ba861757bf4bbd4d45ab7229f.png

SNPViz

http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html

Tags: MSA

Platform: Web

a8e38821bdc5ef3cbe808b34940b57a1.png

SNPitty

https://bitbucket.org/ccbc/snpitty/src/master/

Publication: https://www.jmdjournal.org/article/S1525-1578(17)30166-6/fulltext

Language: R

Tags: Special-purpose, CNV

Platform: Web

cc1eb6a64a8705db65e1d14b9edcf04f.png

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

Tags: Special-purpose, Alignment viewer

a86bb58ef275311f1540a382161fdbf6.png

SFARI

https://gene.sfari.org/database/human-gene/

Tags: Special-purpose, CNV

Platform: Web, Silo

b2a1985b910f73f28296d214b2d43b5c.png

SEQing

https://github.com/malewins/SEQing

Language: Python

Tags: Special-purpose

Platform: Web

f2cff8aabdf8e5913856a795cb119d23.png

SeqCover

https://brentp.github.io/seqcover/#gene=AIFM1

Tags: Special-purpose, Coverage

Platform: Web

9f25f452815728b296c023f4dc56cb60.png

NGB

https://github.com/epam/NGB

Language: Java

Tags: Special-purpose, Alignment viewer

Platform: Web

04ffb7e42539d4498f4d7e5f3aa573ab.png

MapView

https://sites.google.com/site/wjwdavy/

Publication: https://academic.oup.com/bioinformatics/article/25/12/1554/193807

Tags: Special-purpose, Alignment viewer

Note: links in original paper are dead, but URL provided here works

Platform: Desktop

2731a43cae2721be3d56d1172d6c6317.png

Panoptes

https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html

Tags: Special-purpose, Population

Github: https://github.com/cggh/panoptes

8e9787251dc39ced4bdc61da6b2439d9.png

LookSeq

https://www.sanger.ac.uk/tool/lookseq/

Tags: Alignment viewer

Platform: Web

015a1b789d162005afa7fc42dfd9f7ae.png

Locuszoom

http://locuszoom.org/

Tags: GWAS, Population

Note: Also see locuszoom.js http://locuszoom.org/locuszoomjs.php

Platform: Web

4cbad5e34f6c22d9b215592e674469a1.png

IslandPlot

https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565

Language: JS

Tags: Special-purpose

Note: D3, SVG

Platform: Web

1696ff810ce4cd9eaed42ba1dc214c21.png

Introgression browser

https://git.wageningenur.nl/aflit001/ibrowser

Publication: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12800

Language: Python

Tags: SV, Introgression

Platform: Web

1247b0bb2c29b736886db3fc6f533bda.png

InGAP-SV

http://ingap.sourceforge.net/

Tags: SV, Alignment viewer

Platform: Desktop

73b4a6c4fa6b3f5ae8f4541497fd88aa.png

Icarus

http://quast.sourceforge.net/icarus.html

Tags: Assembly QC

Platform: Web

e7c17bf06dc08503f334563e12ccdd4a.png

Human genome dating

https://human.genome.dating/region/chr1_13250000

Tags: Population, GWAS

Note: made with vega/d3

Platform: Web

4ff65cd85d54545bc9a8c405239538f0.png

Hawkeye

Publication: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34 (2007)

Tags: Special-purpose, Alignment viewer, Assembly QC

Platform: Desktop

2e31e51bc5f80e73cf6109b86212cf5d.png

GWAS catalog browser

https://www.ebi.ac.uk/gwas/variants/rs1558902

Tags: Population, LD, GWAS

Platform: Web

1b807784ecdc849bde32c7ec23a0cbe1.png

GTEX Locus browser

https://gtexportal.org/home/locusBrowserPage/ACTN3

Tags: Expression, Linear, LD

Platform: Web

bc0de52eec2d1bd701100174adab371d.png

Gremlin

http://compbio.cs.brown.edu/projects/gremlin/

Tags: SV, Linear

Platform: Web

4e0ab33e25277802e4622f39ac7c33ec.png

Gnomad browser

https://github.com/macarthur-lab/gnomadjs

Tags: Special-purpose, Linear, Population

Platform: Web, Silo

40b0dee13ca6bae79166bab72d7ce3bc.png

Genoverse

https://github.com/wtsi-web/Genoverse

Tags: General, Linear

Platform: Web

5bd33a13adf5ad856baff97720307848.png

GenomeSpy

https://genomespy.app/

Language: JS, WebGL

Tags: CNV, GWAS, Linear, MSA

Platform: Web

b2742a139a0b22607c0a2d2ea7842a20.png

Ribbon

http://genomeribbon.com/

Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa680/5885081?redirectedFrom=fulltext

Tags: SV, Alignment viewer

Github: https://github.com/MariaNattestad/ribbon

Platform: Web

0178385f890c768c75913ad609e49df5.png

Gambit

http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473

Tags: Alignment viewer, Linear

Platform: Desktop

3b0122eebbe66d324e56db1e0a07abc5.png

EaSeq

https://easeq.net/screenshots/

Publication: https://www.nature.com/articles/nsmb.3180

Tags: Special-purpose, Epigenomics

Platform: Desktop

152b9d199d8c26f8819953b15527697c.png

DNASkittle

https://www.dnaskittle.com/

Tags: Special-purpose

Platform: Web

bf8fddac52ea9c8f5b370247c0c4289b.png

D3GB

http://d3gb.usal.es/

Language: JS, D3

Tags: Special-purpose

Platform: Web

90150469abe56b1107e200f77b4de515.png

cnvCurator

http://www.acsu.buffalo.edu/~lm69/cnvCurator

Publication: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0766-y

Language: Java

Tags: CNV, Annotation, Deadlink?

Platform: Desktop

fbd548ca4825a51bc78b1b6ac52f8e7b.png

Chromatic

https://chromatic.nci.nih.gov/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987889/

Language: WASM

Tags: Alignment viewer

Platform: Web

a66a22386a2dba1d6bbfb5546aa7b1a0.png

Chopchop

http://chopchop.cbu.uib.no/results/1611256682447.8318/details/9

Tags: Synthetic biology

e097f3f07e9389f5d42eee2946b24e16.png

Apollo aka WebApollo

https://genomearchitect.readthedocs.io/en/latest/

Language: Java, Groovy, JS

Tags: Gene structure, Annotation, JBrowse integration

Platform: Web

55650dbca435ac70a330831e948242f3.png

Apollo

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/

Language: Java

Tags: Special-purpose, Historical, Deadlink?, Gene structure, Annotation, Comparative

Platform: Desktop

63b65d43329f816a7eee3e3590abbf8c.png

ApE (a plasmid editor)

https://jorgensen.biology.utah.edu/wayned/ape/

Tags: Synthetic biology

Platform: Desktop

97adea254700770e69a941cff270f430.png

seqviz

https://github.com/Lattice-Automation/seqviz#viewer

Tags: Synthetic biology

Platform: Web

c2dee34edf6a4d6f87db4d7e96f73f0a.png

OGDRAW

https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Publication: https://www.biorxiv.org/content/10.1101/545509v1.full.pdf

Tags: Circular, Static

Platform: Web

b73676115e4a28cef807592a1b2bd32e.png

mummer2circos

https://github.com/metagenlab/mummer2circos

Language: Python

Tags: Static

41531227b4e8f2dd19e2a170eb92d12a.png

JupiterPlot

https://github.com/JustinChu/JupiterPlot

Language: Perl

Tags: Circular, Static, Comparative

ff2d3de3bfa8fc61650db083b052f584.png

GenomeProjector

https://github.com/gaou/g-language/wiki

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636772/

Language: Perl

Tags: Circular, Linear

Platform: Desktop

fbd5a88d59195169ebbc5e407797cdde.png

DNAPlotter

https://www.sanger.ac.uk/science/tools/dnaplotter

Language: Java

Tags: Circular

Platform: Desktop

76d01aeaeeaad088ff08bbf2bc0464c1.png

CircosJS

https://github.com/nicgirault/circosJS

Language: JS

Tags: Circular

Platform: Web

87186484bbf0941c6613817e14df8beb.png

Circleator

http://jonathancrabtree.github.io/Circleator/index.html

Language: Perl

Tags: Circular, Static

481e99be9bd03e00371ee88b49fc4617.png

Circa

https://omgenomics.com/circa

Tags: Commercial, Circular

Platform: Desktop

216a50053ec942d97e22e4dacf782e6d.png

BioCircos.js

http://bioinfo.ibp.ac.cn/biocircos/

Language: JS

Tags: Circular

Platform: Web

27784b7ac5e36356cd33e0b11960c104.png

VizAln (from HipSTR)

https://github.com/tfwillems/HipSTR

Tags: Text based

0d538509517a2f48c475ed446f1b5aaf.png

SvABA

https://github.com/walaj/svaba#alignmentstxtgz

Tags: Text based

Platform: CLI

e908dc419a9af699b7310b0fe933dbe2.png

Samtools tview

http://www.htslib.org/

Language: C

Tags: Text based, Alignment viewer

Platform: CLI

864973b7c98bdc973539cd80cb743790.png

Samtools depth visualization

https://twitter.com/yokofakun/status/1178686978541441025

Tags: Text based, Coverage

Platform: CLI, GNUplot

eeedf223f9173ce87dac4f2779b88dbe.png

Rna Alignment Viewers

http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109877/

Language: Perl

Tags: Text based

Platform: CLI

e5670ccfafd9e7bf5f0427c3ecf1f7b8.png

pyBamView

https://mgymrek.github.io/pybamview/

Language: Python

Tags: Alignment viewer, Static

Note: See supplementary info for more figures, supports padded SAM/BAM which is fairly rare

Platform: CLI

62a70d948c01bdf4a052171e64990ca5.png

plotReads

http://campuspress.yale.edu/knightlab/ruddle/plotreads/

Tags: Text based

Platform: CLI, Static

a04eeba18d2efa709f1e8a883e2fe01f.png

Hapviz

https://github.com/ekg/hapviz

Language: C

Tags: Text based

Platform: CLI

79da045a063be3368e0cafafe5d7efb1.png

Bamcov

https://github.com/fbreitwieser/bamcov

Language: C

Tags: Text based, Coverage

Platform: CLI

b81555aca2fb10371d4d702aae084122.png

ASCIIGenome

https://github.com/dariober/ASCIIGenome

Language: Java

Tags: Text based, Alignment viewer

Platform: CLI

48003c00a446541d4ad5665323890303.png

Alv

https://github.com/arvestad/alv

Language: Python

Tags: Text based, MSA

Platform: CLI

4bff4447a325e86c24597f0340848af3.png

Alan

https://github.com/mpdunne/alan

Language: Bash

Tags: Text based, MSA

Platform: CLI

1514da96ec4d65ed569a38601a97cbb3.png

sequence tube map

https://github.com/vgteam/sequenceTubeMap

Language: JS

Tags: Graph

Platform: Web

da172d2165edc4dae3db834ef4fa8033.png

odgi draw + odgi viz

https://odgi.readthedocs.io/en/latest/index.html

Tags: Graph

Note: Example from https://github.com/pangenome/pggb

c11d47e703ecb51b35dede2f1ac7db3f.png

MoMi-G

https://github.com/MoMI-G/MoMI-G/

Language: JS

Tags: Graph, Multi, Alignment viewer, Circular, SV

Platform: Web

dc691473c00484d4301d66488f5f8764.png

graphgenomeviewer

https://cmdcolin.github.io/graphgenomeviewer/

Language: JS

Tags: Graph

Platform: Web

7386172c6707df22fef224c1bc746284.png

gGnomes.js

https://github.com/mskilab/gGnome.js

Language: JS

Tags: SV, CNV, Breakends, Graph

Platform: Web

ab7e24a9ed7d54118772d4187f403c8f.png

gfaestus

https://github.com/chfi/gfaestus

Language: Rust

Tags: Graph

Note: See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4

ab23ccb26405154d2b06bd182d11e8c8.png

Bandage

https://github.com/rrwick/Bandage/

Publication: https://academic.oup.com/bioinformatics/article/31/20/3350/196114

Language: C++

Tags: Graph

Platform: Desktop

72023c74c375e2474f35be18785458fc.png

XMatchView

https://www.bcgsc.ca/resources/software/xmatchview

Tags: Comparative

Platform: Desktop

96d05e11e6d50b61349263f582a5a87e.png

VISTA browser

http://pipeline.lbl.gov/cgi-bin/gateway2

Tags: Comparative

Platform: Web, Silo

b552812027c977b1911a943cdbb50022.png

Tripal MapViewer

https://academic.oup.com/database/article/doi/10.1093/database/baz100/5612723

Tags: Comparative, Ideogram

6a3e782c38d8fb012543f6f0755a864a.png

SynVisio

https://synvisio.github.io/

Language: JS

Tags: Comparative, Linear, Dotplot

817da2e68b1a51a2848a2a7b642c2094.png

SynTView

http://hub18.hosting.pasteur.fr/SynTView/documentation/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849071/

Tags: Comparative, Dotplot, Linear

Platform: Desktop, Web, Flash

4bdb1a3f8624e3f0d7bcfb13492b0489.png

Synteny browser

https://github.com/TheJacksonLaboratory/syntenybrowser

Tags: Comparative

Platform: Web

f6593a4314bb14b61779f696d63f750e.png

Synima

https://github.com/rhysf/Synima

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697234/

Language: Perl

Tags: Comparative

Platform: CLI

70ebefebd1ae2d0576f16e7019193f8b.png

SyMap

http://www.agcol.arizona.edu/software/symap/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105427/

Tags: Comparative, Dotplot, Linear

Platform: Desktop

7c68255feacf40e1b2ca5ee62da0dd49.png

progressiveMauve viewer

http://darlinglab.org/mauve/user-guide/viewer.html

Tags: Comparative

Platform: Desktop

9035c665572ad5642e05038432af703f.png

syri/plotsr

https://schneebergerlab.github.io/syri/plotsr.html

Language: Python

Tags: Comparative, Linear

d70f8194989c242437a1e654d03e91fd.png

Parasight

https://baileylab.brown.edu/parasight/galframe.html

Language: Perl

Tags: Comparative

Note: Examples at https://ratparalogy.gs.washington.edu/

3b6461a71fea49cd637148554482d273.png

pafr

https://github.com/dwinter/pafr

Language: R

Tags: Comparative, Dotplot, Linear

8b394d7e6d938e6b928a55996f95522a.png

OMA local synteny browser

https://omabrowser.org/oma/synteny/ADH1A_HUMAN/

Tags: Comparative, Gene order

Platform: Web, Silo

67546c106c249fd392fa8aebc7d55c0c.png

Multiple genome viewer

http://www.informatics.jax.org/mgv/

Tags: Comparative

Platform: Web, Silo

4252178ef5d3cc326711e0beb129a867.png

MizBee

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

Publication: https://ieeexplore.ieee.org/document/5290692

Language: Processing

Tags: Comparative

Platform: Desktop

48c53a6f97492e544a3b4924dd1da353.png

MCScanX

https://github.com/wyp1125/MCScanX

Language: Perl

Tags: Comparative, Dotplot, Circular, Linear, Ideogram

Platform: CLI

e6f8e67adfa4d738f6dc90c726aa535f.png

MCScan (python version)

https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

Language: Python

Tags: Comparative, Dotplot, Linear

Platform: CLI

7db6c1892a881f0b10889338c6dd1d72.png

mauve-viewer

https://github.com/nconrad/mauve-viewer

Language: JS

Tags: Comparative

Platform: Web

3d2c4c3474dad1e31c995af380748f09.png

GIVE

https://zhong-lab-ucsd.github.io/GIVE_homepage/

Language: JS

Tags: Comparative, Linear, Quantitative

Platform: Web

99d1e2deb21ee7b6d6e82bb5ebb6f023.png

gggenomes

https://github.com/thackl/gggenomes

Language: R

Tags: Comparative

Platform: Package

11ffc1beb9aab1446461666c2c7e7e88.png

Genomicus

https://www.genomicus.biologie.ens.fr/genomicus/

Tags: Comparative, Ideogram, Dotplot

Platform: Web, Silo

ec92ea57f590e023ef91614d45b71f13.png

Genome-plots-processing

https://github.com/filip-husnik/genome-plots-processing

Language: Processing

Tags: Comparative

941045123d232f48de5523524b06b8fe.png

Genome Context Viewer

https://www.legumefederation.org/gcv/phytozome_10_2/

Tags: Comparative, Gene order

Platform: Web, Silo

002663fdd18ed72707049bf0ddad76e9.png

GBrowse_syn

http://gmod.org/wiki/GBrowse_syn

Language: Perl

Tags: Comparative

Platform: Web

156fcc85c7a4f44e4fc914352abd298f.png

Edinburgh-Genome-Foundry/DnaFeaturesViewer

https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer

Publication: https://academic.oup.com/bioinformatics/article-abstract/36/15/4350/5868559?redirectedFrom=PDF

Language: Python

Tags: Microbiology, Synthetic biology

Platform: Desktop

0a89133c69cf45f4bd8e8f716cad80ae.png

EasyFig

https://mjsull.github.io/Easyfig/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065679/

Language: Python

Tags: Comparative

Platform: CLI

3d09e9e44f861f273c1fbcd0be40fcbe.png

Cvit.js

https://github.com/LegumeFederation/cvitjs

Tags: Comparative

Platform: Web

4afd5c4de93f1889abbf0e33db784790.png

CVit

https://sourceforge.net/projects/cvit/

Language: Perl

Tags: Comparative

Platform: Web

98330547174057f02848804474864c53.png

CrossBrowse

https://github.com/shenkers/CrossBrowse

Publication: https://www.biorxiv.org/content/10.1101/272880v1.full

Language: Java

Tags: Comparative

Platform: Desktop

dde1daed8fa281e25faa65f344e853de.png

Comparative assembly hub / "snake track"

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/

Tags: Comparative, UCSC integration

Platform: Web

0d1c76819c09bc2a0f6243c72323b888.png

CoGe

https://genomevolution.org/coge/

Language: Perl

Tags: Comparative, Dotplot, Linear, JBrowse integration

Platform: Web, Silo

080f976fdfa6f395c3f5da9e50e4be34.png

CMap

http://gmod.org/wiki/CMap

Language: Perl

Tags: Comparative

Platform: Web

48407c870a2ba9d13f67b297536df04f.png

Chromatiblock

https://github.com/mjsull/chromatiblock

Publication: https://www.biorxiv.org/content/10.1101/800920v2.full.pdf

Language: Python

Tags: Comparative, Pangenome

Platform: Web

074c2def07fa85490fa2c5193e2424b9.png

Biodalliance comparative demo

http://biodalliance.org/dev/test-comparative.html

Language: JS

Tags: Comparative

Platform: Web

1aa5cf2ec4ac40e1db35bb53168988a7.png

Artemis comparison tool (ACT)

https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

Language: Java

Tags: Comparative

Platform: Desktop

db7feac78cd77d02c22ba964a5ba0246.png

AliTV

https://alitvteam.github.io/AliTV/d3/AliTV.html

Tags: Comparative

Platform: Web

d9281725a01ee7815c71f7fadd95ac36.png

Aequatus

https://github.com/TGAC/Aequatus

Tags: Comparative, Deadlink?

Platform: Web, Silo

d3d966f33afbedff9c0a3aeb7bdbf03e.png

trackViewer

https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html

Language: R

Tags: Static, Lollipops, Quantitative

590ed652c6b99d748fa9f756cc0f59e7.png

TnT

https://tnt.marlin.pub/articles/introduction

Language: R, JS

Tags: Gene structure

Platform: Web, Interactive

b8a9937ad5bd954458a236368fb5eb35.png

svviz2

https://github.com/nspies/svviz2

Publication: https://pubmed.ncbi.nlm.nih.gov/26286809/

Language: Python

Tags: Static, SV, Insertion

8934261ccb3ff85e9b956e010ae5d937.png

svviz

https://github.com/svviz/svviz

Publication: https://pubmed.ncbi.nlm.nih.gov/26286809/

Language: Python

Tags: Static, SV, Insertion

08aeaa7ed07224115da3aada4eaf5130.png

svv

https://github.com/ryanlayer/svv

Language: Python

Tags: Static, SV, Coverage

58ac705ff28308f48848000a84b9ccb0.png

svist4get

https://link.springer.com/article/10.1186/s12859-019-2706-8

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2706-8

Language: Python

Tags: Static

0f15b524408dc43a719bb53718e42d51.png

Sushi

https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

Language: R

Tags: Static, Multi

61e1cbfe67ef53fd883e5b857081f553.png

Spliceclust

https://github.com/pkimes/spliceclust

Language: R

Tags: Static, Splicing

5f1d814a212bb8ca6b4186038cb9ed06.png

SparK

https://github.com/harbourlab/SparK

Publication: https://www.biorxiv.org/content/10.1101/845529v1.full.pdf

Language: Python

Tags: Static, Hi-C, Quantitative

f78000a06ab7f426e9f7fb2eac046c2a.png

shinyChromosome

http://150.109.59.144:3838/shinyChromosome/

Publication: https://www.sciencedirect.com/science/article/pii/S1672022919301883

Language: R, Shiny

Tags: Dotplot, Linear, Ideogram

Platform: Web

42082dbea3ae4fe1e231e06a404a042c.png

shabam

https://github.com/dlrice/shabam

Language: Python

Tags: Static

e13a81e6b27619e9de4acbddbcce1709.png

SashimiPlot

https://miso.readthedocs.io/en/fastmiso/sashimi.html

Language: Python

Tags: Static, Expression, Splicing

d6e0f3ca9409b7383a88f882378b139a.png

Samplot

https://github.com/ryanlayer/samplot

Language: Python

Tags: Static, SV, Alignment viewer

13518046908748c1542298552feaa356.png

RepViz

https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z

Language: R

Tags: Static, Quantitative

Github: https://github.com/elolab/RepViz

df9455b9205c02a0b871aab32b68f3ac.png

RACER

https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html

Language: R

Tags: Static, GWAS

bb3d2697ec4b3e0b226a645153d067c3.png

pyGenomeTracks

https://github.com/deeptools/pyGenomeTracks

Language: Python

Tags: Static, Hi-C

dbb8ec488ce70d518730d8198ae1bff2.png

PureScript genetics browser

https://github.com/chfi/purescript-genetics-browser

Language: Purescript

Tags: GWAS

Platform: Web

b23deea62fad1914bb8034655010a21c.png

pauvre

https://github.com/conchoecia/pauvre

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/

Language: Python

Tags: Static, Misc QC, Comparative

Platform: CLI

32d7c22d1bc92c03da98b98add280c9f.png

Pairoscope

http://pairoscope.sourceforge.net/

Language: C++

Tags: Static, SV

71d77ab560d68fc7b9008be7f11a6136.png

Millefy

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053140/

Language: R

Tags: Single cell

Platform: Package

35846d4d19aff566d8a03d4af24fda39.png

Methplotlib

https://www.biorxiv.org/content/10.1101/826107v1.full.pdf

Language: Python

Tags: Static, Epigenomics, Methylation

03cf31250af2afb3c7f63644d01372fe.png

Mason

http://www.yeastrc.org/mason/

Tags: Static, Protein

Platform: Web

3d190653e8bd63db890eff3c01eb4b43.png

Lollipops

https://github.com/joiningdata/lollipops

Language: Go

Tags: Static, Protein, Lollipops

286a9f80ff6384fbfebb1382088f139c.png

JVarKit/BamToSVG

http://lindenb.github.io/jvarkit/BamToSVG.html

Language: Java

Tags: Static, Alignment viewer

2844ecaae5749483746677c15daccd1c.png

HiCPlotter

https://github.com/kcakdemir/HiCPlotter

Language: Python

Tags: Static, Hi-C

73d1f9ba73bfbe9f58e50639d575c0de.png

Hagfish

https://github.com/mfiers/hagfish/wiki/Plots

Language: Python

Tags: Static, Coverage

f28f19c8866bbf280c4d0c9c33e45cd1.png

Gviz

https://bioconductor.org/packages/release/bioc/html/Gviz.html

Language: R

Tags: Static, Alignment viewer, Quantitative, Multi

2f7b6dc635542dffe82f7b457c19138b.png

gtrellis

http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html

Language: R

Tags: Static, Ideogram, Quantitative, CNV

a173c89a21590031dd3fb67df76b076e.png

GSSPlayground

https://github.com/orangeSi/GSSplayground

Language: Perl

Tags: Comparative, Static, Alignment viewer

19f8b6520679fa0b0dc89edce1c4e20a.png

GGsashimi

https://github.com/guigolab/ggsashimi

Language: R

Tags: Static

324a33d0dc0f7c1f52527b37159ddc0a.png

GGgenes

https://github.com/wilkox/gggenes

Language: R

Tags: Static, Comparative

b0a5c0a91b044ed5a2c7772fbdccb046.png

ggbio

http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf

Publication: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-8-r77

Language: R

Tags: Static, Ideogram, Circular, Multi

342a2690cd8bf7dc18ab4cbd0c8caeda.png

genoPlotR

http://genoplotr.r-forge.r-project.org/

Language: R

Tags: Static, Comparative

693e85f78aaf991b636f235bafa1efb7.png

GenomeView (java app)

https://genomeview.org/content/quick-start-guide

Language: Java

Tags: Alignment viewer

fd1b85b1036e91d193fb3ff207a9bf30.png

GenomeView

https://github.com/nspies/genomeview

Language: Python

Tags: Static, SV, Alignment viewer

5ebd5d56004a6d5f0ba39e8e32fc160c.png

GenomeTools

http://genometools.org/

Language: C

Tags: Static, Gene structure

af63764eb44cbd066b7a43398b342d4b.png

Genome STRiP

http://software.broadinstitute.org/software/genomestrip/

Tags: Static

e9d7e0d1c6344f4270923dc2186c7da2.png

Geneviz

https://jrderuiter.github.io/geneviz/usage.html

Language: R

Tags: Static, Gene structure

b5fa55b79141a53b1033f49ecf0bbdc1.png

FeatureViewer

https://github.com/calipho-sib/feature-viewer

Tags: Static, Gene structure

Platform: Web

b5b2110f1dc88311dd955bf05f905197.png

ExonIntron

http://wormweb.org/exonintron

Tags: Static, Gene structure

b6b3c109aa65f433b30f9d5bf70e3f5a.png

DNAPlotLib

https://github.com/VoigtLab/dnaplotlib

Language: Python

Tags: Static, Synthetic biology

536400d0b3be2ede3e5403cdc2dea333.png

CNVpytor

https://github.com/abyzovlab/CNVpytor

Language: Python

Tags: Static, CNV

4e492c6206d0a831ba522506f46618aa.png

CNVPlot

https://github.com/dantaki/CNVplot/

Language: R

Tags: Static, CNV

73394b93f759bb6e039b9f228cec98ac.png

CNView

https://github.com/RCollins13/CNView

Language: R

Tags: Static, CNV

422c4f1e85e014ce6b39edc09a3f55f1.png

Chimeraviz

https://github.com/stianlagstad/chimeraviz

Language: R

Tags: Gene fusion, Circular, Linear

5dc0874c0324873e56a911176fc23e6b.png

ChIA-Pipe

https://github.com/TheJacksonLaboratory/ChIA-PIPE

Publication: https://www.biorxiv.org/content/10.1101/506683v1.full.pdf

Tags: Static, Epigenomics

25434ea7a65e2c2afbbc191875c786aa.png

BAMSnap

https://github.com/parklab/bamsnap

Language: Python

Tags: Static, Alignment viewer

7c5c3d2d580617b68f62ac3b341d8fff.png

BAMScale

https://github.com/ncbi/BAMscale

Publication: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00343-x

Language: C, R

Tags: CNV, Static

6301328e42ad5f66387d46a53971798f.png

CNVkit

https://cnvkit.readthedocs.io/en/stable/plots.html

Publication: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873

Language: Python

Tags: CNV

Github: https://github.com/etal/cnvkit

79eb6aac4284dc20401e010ea6437cc5.png

aCNVViewer

https://github.com/FJD-CEPH/aCNViewer

Publication: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189334

Language: Python

Tags: CNV, Static

1c8c3608fe1903c7f31c1e11fa012e0c.png

Wasabi

http://wasabiapp.org/

Tags: MSA

Platform: Web

2f4c98d0d9cafe855cfe22d3450e61fe.png

TeXShade

http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf

Tags: MSA

Platform: Desktop

930ccf31f537782a7e17d89c5a4a8e13.png

STRAP

http://www.bioinformatics.org/strap/

Tags: MSA

Note: also see AA

Platform: Web, Applet

2a4f0a24e112e751234ef107b5063c5c.png

seqotron

https://github.com/4ment/seqotron

Language: Objective-C

Tags: MSA

Platform: Desktop

dc3c258cedb6b74f16fee891f616437d.png

react-msaview

https://github.com/GMOD/react-msaview

Language: JS, React

Tags: MSA

545c61ef5c83d9db38ab3db87ff2bcb6.png

React MSAViewer

https://github.com/plotly/react-msa-viewer

Language: JS, React

Tags: MSA

Platform: Web

0f80669cb81600e1ffb27c8bc8e93bff.png

pymsaplotter

https://github.com/orangeSi/pymsaploter

Language: Python

Tags: MSA

a22e24ec3ba1d70940d9ee0c929ddae1.png

pyBoxshade

https://github.com/mdbaron42/pyBoxshade

Language: Python

Tags: MSA

Note: also see boxshade

Platform: Desktop

c7540b5c9aa7e01276e15ea1ee890ed8.png

NCBI MSA Viewer

https://www.ncbi.nlm.nih.gov/projects/msaviewer/

Tags: MSA

Platform: Web, CGI

5cc26ed084b1ae1b452b8bbf79446eb3.png

MView

https://www.ebi.ac.uk/Tools/msa/mview/

Tags: MSA

Platform: Web

fd3c06a2c9087bcfd95b420b81349564.png

msaR

https://github.com/zachcp/msaR

Language: R, JS

Tags: MSA

Note: uses BioJS/MSA

Platform: Desktop, R/htmlwidget

9b31f57fc9905ac9230e00a909d2da7e.png

MSABrowser

https://thekaplanlab.github.io/

Tags: MSA

Platform: Web

747c15220a16f2b3aecefc4de23639f1.png

LogoJS

https://logojs.wenglab.org/app/gallery/

Language: JS

Tags: Logo

Platform: Web

17a3e14944712022aaf3ee3a02eef68c.png

JSAV

http://www.bioinf.org.uk/software/jsav

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304231/

Language: JS

Tags: MSA

Platform: Web

78e40bec9f6a2433eadb083b40c4aad4.png

Jalview

https://www.jalview.org/

Language: Java

Tags: MSA

Platform: Desktop

9ac97d6abd9c43fd5015dd84ec6b5ffa.png

ESPript

http://espript.ibcp.fr/ESPript/ESPript/

Tags: MSA

Platform: Desktop

9a4a30fa3e4da36e5dbb51e71d3371dc.png

Boxshade

https://embnet.vital-it.ch/software/BOX_form.html

Tags: MSA

Platform: Web

29f82e2a958bf1959839bd6194ea1d5d.png

BioJS/MSA

https://msa.biojs.net/

Publication: https://academic.oup.com/bioinformatics/article/32/22/3501/2525598?login=true

Tags: MSA

Platform: Web

8555ccf5e54052e1addf258c916d1355.png

AliView

http://www.ormbunkar.se/aliview/

Language: Java

Tags: MSA

Platform: Desktop

ed5c7e64c1d2d44355317f6dda85ab91.png

AlignmentViewer

https://alignmentviewer.org/

Tags: MSA

Platform: Web

9461cb86b630b08ace71725ae0e04d03.png

AlignmentComparator

http://bioinfweb.info/AlignmentComparator/

Language: Java

Tags: MSA

Note: Uses http://bioinfweb.info/LibrAlign/

f295928ae2da72618dc711dc5cb025ad.png

alignment.js

https://github.com/veg/alignment.js

Tags: MSA

Platform: Web

0fa8be4f1676cdd947d45476c1fb99b5.png

abrowse

https://github.com/ihh/abrowse

Tags: MSA

Platform: Web

4ec8b948aca28f1267b0581799f884d8.png

AA

http://www.bioinformatics.org/strap/aa

Tags: MSA

Note: also see STRAP

Platform: Web

f7b6d04da64239f7f2b0b87cbe6e10c3.png

Bionano

https://bionanogenomics.com/technology/structural-variation/

Tags: Commercial, SV

ccd8f9a44a2a1abb77bbe89f7ccf140c.png

Strand NGS

https://www.strand-ngs.com/

Tags: Commercial

4d773b1ab22d5e0fca41c3ad9be2d6b5.png

SnapGene

https://www.snapgene.com/

Tags: Commercial

0a0fc6ff1623bc776aa2250a1a3ed567.png

Persephone

https://persephonesoft.com/

Tags: Commercial, Comparative

b857ba2972d3b2118c53b9cb481480f5.png

MacVector

https://macvector.com/

Tags: Commercial

8c85553dc26d9e28f51fb1f345a39642.png

Lucid viewer

https://lucidalign.com/

Tags: Commercial

2330b1c5ac7f8ae51d8862caf43defe6.png

Golden Helix

http://goldenhelix.com/GenomeBrowse/

Tags: Commercial

20f2f8d54240b85146be4c1ca81c6045.png

Genestack

https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/

Tags: Commercial

65b6d4ec25c42e52fb23a019bc36398d.png

Geneious

https://www.geneious.com/

Tags: Commercial, Synthetic biology

1dc2cc7b14d140feb47b1dd367bc99f1.png

DNASTAR

https://www.dnastar.com/

Tags: Commercial

358cb89a3f67780cd7e48336936feccb.png

CLC Genomics workbench

https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/

Tags: Commercial, SV

0249d07ff7980119121474dcd27a4c3c.png

Benchling

https://www.benchling.com/

Tags: Commercial, Synthetic biology

72ed8c0ee2b2835d645f347b9b644316.png

ATCC Genome Portal (American Type Culture Collection)

https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser

Tags: Commercial, Microbiology

90eee23fb035e39cc731dd5d582494d4.png

Alamut

https://www.interactive-biosoftware.com/alamut-visual/

Tags: Commercial

142dabc122f48e26adc65dcb8c8f2ba8.png

10x genomics/Loupe

https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants

Tags: Commercial

2f9d92f35257eb64b3c0809805d58d73.png

Note: if you would like your tool removed or screenshot removed (for copyright purposes for example) let me know

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clinker:基因簇比较图生成器
03-04
熟料 基因簇比较图生成器 它是什么？ 熟料是用于轻松生成出版物质量的基因簇比较图的管道。 给定一组GenBank文件，clinker将自动提取蛋白质翻译，在每个簇中的序列之间进行全局比对，根据簇的相似性确定最佳的显示顺序，并生成可进行广泛调整的交互式可视化（使用 ）。被导出为SVG文件。 安装 熟料可以通过pip直接安装： pip install clinker 通过从GitHub克隆源代码： git clone https://github.com/gamcil/clinker.git cd clinker pip install . 或者，通过conda： conda create -n clinker -c conda-forge -c bioconda clinker-py conda activate clinker 引文 如果您发现熟料有用，请引用： clink
基因组工具：GenomeTools基因组分析系统
01-30
Genome工具 GenomeTools基因组分析系统是一个免费的生物信息学工具集合（在基因组信息学领域），组合成一个名为gt二进制文件。 它基于一个名为libgenometools的C库，该库包含用于高效，便捷地实现序列和注释处理软件的各种类。 如果您对基因预测感兴趣，请查看 。 GenomeTools设计为可在每个POSIX兼容的UNIX系统上运行，例如Linux，Mac OS X和OpenBSD。 Debian（正在测试）和Ubuntu（正在运行rar和更高版本）的用户只需使用apt就可以安装最新的稳定版本，例如 % apt-get install genometools 安装gt可执行文件。 要安装库和开发头，请使用 % apt-get install libgenometools0 libgenometools0-dev 代替。 可从GitHub获得 。 有关如何自行构建源的说明，请查看文件。 在大多数情况下（例如在64位Linux系统上），类似 $ make -j4 应该足够了。 在32位系统上，添加32bit=yes选项。 如果您没有安装Cairo库及其开发标
IGV.js | 载入自己下载的gtf文件
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IGV.js 的自定义
从基因组可视化工具——circos说起，circos安装
weixin_34072159的博客
07-28 644
    这是博客改版的第一篇博文，选择最近使用的生物信息学软件——circos开始写起。circos是用perl写的生物软件，从发表的文章来看     学习circos主要是熟悉配置文件的编辑方法，搞清楚其中的标签、参数的含义。只有完全清楚了这些东西才能够轻松自如的让circos绘制出主要用于基因组序列的可视化（绘制基因组圈图），至少目前我是用来干这个事情的。现在circos也被其他领域...
genome-tools:基因组数据的处理和绘图工具
05-04
基因组工具 有关使用情况的示例，请参阅。 如果人们觉得这有用，我将添加更多内容/示例。 注意：应该同时适用于python版本2和3。 安装 克隆git仓库 [jvierstra@test0 ~]$ module load git [jvierstra@test0 ~]$ mkdir -p ~/.local/src && cd ~/.local/src [jvierstra@test0 src]$ git clone https://github.com/jvierstra/genome-tools.git 编译并本地安装python包 [jvierstra@test0 src]$ cd genome-tools [jvierstra@test0 genome-tools]$ python setup.py install --user
GenVisR:基因组数据可视化
05-02
GenVisR 请引用：“斯基德莫尔等人2016 GenVisR：基因组可视化中的R 32的生物信息学，3012-3014” 直观地可视化和解释来自高通量基因组技术的数据仍然具有挑战性。 “ R中的基因组可视化”（GenVisR）试图通过提供高度可定制的出版物质量图形来减轻这种负担，这些图形支持多个物种，并且主要关注人群水平（即多个样本/患者）。 GenVisR尝试保持高度的灵活性，同时利用ggplot2和生物导体的功能来实现此目标。 从Bioconductor安装 对于大多数用户，我们建议从Bioconductor的发行分支安装GenVisR，使用此方法的安装说明可在Bioconductor的上找到。 请注意，GenVisR导入了一些具有“系统要求”的软件包，在大多数情况下，这些要求已被安装。 如果不是，请按照R终端中的说明安装这些软件包。 简要地说，这些软件包是：“ libcurl
探索基因组数据的可视化新境界——GenomeView
gitblog_00033的博客
06-15 372
探索基因组数据的可视化新境界——GenomeView 项目地址:https://gitcode.com/nspies/genomeview 1、项目介绍 在生命科学研究中，对基因组数据的理解和解析是至关重要的。GenomeView 是一个用 Python 编写的高效模块，专为展示和探索复杂基因组数据而设计。通过直观的图形界面，研究人员可以轻松地查看、比较和分析大量的生物信息学数据。 这个壮观的可...
数据可视化
weixin_48995695的博客
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excel提供了商业标准的可视化内容，但总显笨拙。也不希望excel形成垄断，到时候坐地起价。程序员的求知天性，也要求随心所欲得设计，总希望是设置参数而不是选项，是调用函数而不是下拉列表框。自由是要付出代价的，就像到地摊上淘A货，或者自已起炉灶。 总会用种种问题，不能显示中文，代码页不同，不能调整大小。众多的媒体推送，看着眼花缭乱。一看就会，一做就废。都成股市里的庄家，套路满满。听话就有糖吃的时代一去不复返。 Matplotlib 默认情况不支持中文，我们可以使用以下简单的方法来解决。这里我们使用思源黑体
CLC Genomics Workbench
08-30
- *1* *2* *3* [346个基因组可视化工具一网打进！](https://blog.csdn.net/qazplm12_3/article/details/121155034)[target="_blank" data-report-click={"spm":"1018.2226.3001.9630","extra":{"utm_source":"vip_...
文本比较在生物信息学中的威力：序列比对和基因组分析，探索生命奥秘
[文本比较在生物信息学中的威力：序列比对和基因组分析，探索生命奥秘](https://img-blog.csdnimg.cn/c66ba91b8263469799d51925ccde3330.png) # 1. 文本比较在生物信息学中的基础 文本比较在生物信息学中至关重要，...
自动化挖掘视觉相关关系
10403VrR-VG：重新聚焦视觉相关关系*梁元智1，2，白...由于非视觉信息的高可预测性，现有方法倾向于拟合统计偏差，而不是为了进一步发展中国家，光对火车对人走向平台人脸火车的关系，我们提出了一种新的方法来自动化
genometools:Genome工具
05-14
Genome工具 最新的 开发 GenomeTools是用于分析基因组数据的Python类，函数和脚本的集合。 该库与Python 2.7和3.5兼容。 安装 $ pip install genometools 演示笔记本 ：GenomeTools命令行脚本 文献资料 可在ReadTheDocs上找到GenomeTools文档。 版权和许可 版权所有（c）2015、2016 Florian Wagner GenomeTools is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License, Version 3, as published by the Free Software Foundation. This progr
GMOL:3D基因组结构可视化工具-开源
04-28
GMOL是设计用于可视化3D基因组结构的应用程序。 它允许用户以多种尺度查看基因组结构，包括：全局，染色体，基因座，纤维，核小体和核苷酸。 该软件是基于Cheng教授团队的预先存在的Jmol软件包构建的。 该软件由美国密苏里大学计算机科学系的程健林教授的生物信息学，数据挖掘和机器学习实验室开发。 该项目得到了美国国家科学基金会（授权号：DBI1149224）的支持。 如果您在研究中使用GMOL，请引用：Nowotny，Jackson，Avery Wells，Oluwatosin Oluwadare，徐凌飞，曹仁志，Tuan Trieu，何晨风和郑建林。 “ GMOL：用于3D基因组结构可视化的交互式工具。” 科学报告6（2016）：20802。
一个可扩展基于python的基因组学可视化引擎
08-11
一个可扩展基于python的基因组学可视化引擎
基因分析工具
11-08
序列分析工具，科学实验工具实用小软件，在自然领域中实用较多，请留意哦
genome-tools-开源
04-28
Genome-tools提供了灵活的工具和简单的API，可对以标准Genbank格式发布的基因组进行基因组序列处理。 还提供基于CGI的Web界面。 请引用：Lee W.，Chen SL BioTechniques 33：1334-1341（Dec 20
脑科学磁共振成像（MRI)初学者必看——功能脑网络、小世界网络、FDR校正、脑电信号频率变换、模板、假设检验、广义线性模型、独立成分分析、影像组学、任务态和静息态方法汇总
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磁共振成像初学者必看一、浅谈功能脑网络二、不同模态脑网络的构建功能脑网络结构脑网络白质纤维束脑网络加权网络二值网络三、趣谈散点图与相关系数四、脑电信号频域变换五、fMRI中的FDR校正六、模板（mask）1、模板(mask )往往是与ROI联系在一起的2、mask作用的原理3、常见的mask七、假设检验和效果量八、组水平标准化九、由 ALFF 说开去十、计算机存取MRI影像的那些事十二、Linux基础命令十三、浅谈标准空间模板和空间变换一：标准空间模板二：空间变换十四 、 功能连接十五、大脑激活与功能连接的
新工具：轻松可视化基因组，部分功能超IGV～
qq_21478261的博客
06-30 330
figeno擅长可视化三代long reads、跨区域基因组断点视图（multi-regions across genomic breakpoints）、表观组数据（HiC、ATAC-seq和ChIP-seq等）可视化、WGS中的CNV和SV可视化等。支持三代测序数据可视化（Nanopore， PacBio数据），例如， base modification（5mC、hmC、6 mA、5mC、5hmC)）HiC data across breakpoints，展示跨基因组区域的染色质相互作用，
使用Gviz包实现基因组数据可视化
Xingze_Li
01-07 4679
Gviz包介绍 Gviz软件包简介 Gviz软件包旨在提供一个结构化的可视化框架，以沿着基因组坐标绘制任何类型的数据。它还允许整合来自UCSC或ENSEMBL等来源的公开基因组注释数据。 与大多数基因组浏览器一样，单独类型的基因组特征或数据由单独的Track表示。 默认情况下，Gviz 检查所有提供的染色体名称在 UCSC 上的有效性（染色体必须以 chr 字符串开头）。可以决定通过调用 options(ucscChromosomeNames=FALSE) 来关此功能 在以下示例中，将利用小鼠 mm9.
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