Most popular bioinformatics repositories and open source projects

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

circosJS

d3 library to build circular graphs

118 488 488

DnaFeaturesViewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank...

75 484 484

dash-bio

Open-source bioinformatics components for Dash

188 480 480

megahit

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

130 479 479

clinker

Gene cluster comparison figure generator

56 450 450

cutadapt

Cutadapt removes adapter sequences from sequencing reads

123 446 446

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

edlib

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

151 440 440

biotite

A comprehensive library for computational molecular biology

67 432 432

Sniffles

Structural variation caller using third generation sequencing

75 430 430

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

123 425 425

cdk

The Chemistry Development Kit

153 422 422

jvarkit

Java utilities for Bioinformatics

129 420 420

redun

Yet another redundant workflow engine

31 420 420

react-cytoscapejs

React component for Cytoscape.js network visualisations

61 418 418

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

anndata

Annotated data.

124 397 397

dada2

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

135 395 395

PostGUI

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

45 387 387

sourmash

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

69 379 379

anvio

An analysis and visualization platform for 'omics data

129 377 377

maftools

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

211 377 377

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

65 376 376

pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram)

16 376 376

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

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

arvados

An open source platform for managing and analyzing biomedical big data

110 347 347

seqan3

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

76 342 342

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

176 340 340

Deep_learning_examples

Examples of using deep learning in Bioinformatics

124 338 338

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA...

58 338 338

minigraph

Proof-of-concept seq-to-graph mapper and graph generator

36 335 335

RNAseq-workflow

A repository for setting up a RNAseq workflow

168 332 332

cyvcf2

cython + htslib == fast VCF and BCF processing

63 327 327

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

57 326 326