Most popular bioinformatics repositories and open source projects

redun

Yet another redundant workflow engine

53 556 556

biostar-central

Biostar Q&A

231 553 553

bioawk

BWK awk modified for biological data

116 552 552

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignmen...

171 548 548

plantcv

Plant phenotyping with image analysis

244 548 548

bowtie2

A fast and sensitive gapped read aligner

153 540 540

biojava

:book::microscope::coffee: BioJava is an open-source project dedicated...

367 534 534

poly

A Go package for engineering organisms.

53 527 527

GraKeL

A scikit-learn compatible library for graph kernels

92 521 521

dash-cytoscape

Interactive network visualization in Python and Dash, powered by Cytos...

118 517 517

sambamba

Tools for working with SAM/BAM data

96 508 508

nanopolish

Signal-level algorithms for MinION data

157 492 492

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

132 492 492

circosJS

d3 library to build circular graphs

118 488 488

dash-bio

Open-source bioinformatics components for Dash

188 480 480

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

130 479 479

anvio

An analysis and visualization platform for 'omics data

149 476 476

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studi...

223 459 459

PostGUI

A React web application to query and share any PostgreSQL database.

55 455 455

cutadapt

Cutadapt removes adapter sequences from sequencing reads

123 446 446

quast

Genome assembly evaluation tool

86 445 445

jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HT...

197 444 444

hh-suite

Remote protein homology detection suite.

120 444 444

Dash.jl

Dash for Julia - A Julia interface to the Dash ecosystem for creating...

41 443 443

biotite

A comprehensive library for computational molecular biology

67 432 432

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creatin...

32 431 431

Sniffles

Structural variation caller using third generation sequencing

75 430 430

cdk

The Chemistry Development Kit

153 422 422

jvarkit

Java utilities for Bioinformatics

129 420 420

react-cytoscapejs

React component for Cytoscape.js network visualisations

61 418 418

arvados

An open source platform for managing and analyzing biomedical big data

125 409 409

cobrapy

COBRApy is a package for constraint-based modeling of metabolic networ...

205 406 406

pyfaidx

Efficient pythonic random access to fasta subsequences

69 399 399

homelab_status_page

🦒🦒🦒 Fool-proof, robust, and easy-to-use (robotic-UI-Research)🦒🦒🦒...

3 398 398

anndata

Annotated data.

124 397 397

dada2

Accurate sample inference from amplicon data with single nucleotide re...

135 395 395

awesome-bioie

🧫 A curated list of resources relevant to doing Biomedical Informatio...

34 385 385

awesome-biology

Curated (meta)list of resources for Biology.

49 383 383

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets...

69 379 379

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

65 376 376

foldseek

Foldseek enables fast and sensitive comparisons of large structure set...

53 366 366

manta

Structural variant and indel caller for mapped sequencing data

137 362 362

dance

DANCE: a deep learning library and benchmark platform for single-cell...

38 361 361

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

42 356 356

hap.py

Haplotype VCF comparison tools

115 353 353

awosome-bioinformatics

A curated list of resources for learning bioinformatics.

108 352 352

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications t...

73 352 352

pyGenomeViz

A genome visualization python package for comparative genomics

21 345 345

seqan3

The modern C++ library for sequence analysis. Contains version 3 of th...

76 342 342

fgbio

Tools for working with genomic and high throughput sequencing data.

75 341 341