Most popular bioinformatics repositories and open source projects

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  

maftools

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

223   459   459  

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  

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  

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  

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