Most popular bioinformatics repositories and open source projects

cs-video-courses

List of Computer Science courses with video lectures.

9262   68452   68452  

dash

Data Apps & Dashboards for Python. No JavaScript Required.

2114   21994   21994  

biopython

Official git repository for Biopython (originally converted from CVS)

1634   3665   3665  

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to...

741   3359   3359  

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

629   3331   3331  

nextflow

A DSL for data-driven computational pipelines

688   2947   2947  

awesome-single-cell

Community-curated list of software packages and data resources for sin...

852   2566   2566  

scanpy

Single-cell analysis in Python. Scales to >100M cells.

620   2059   2059  

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filt...

302   1541   1541  

bioconda-recipes

Conda recipes for the bioconda channel.

2659   1493   1493  

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequen...

375   1479   1479  

gatk

Official code repository for GATK versions 4 and up

545   1460   1460  

scispacy

A full spaCy pipeline and models for scientific/biomedical documents.

196   1428   1428  

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

166   1420   1420  

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long...

538   1319   1319  

seqtk

Toolkit for processing sequences in FASTA/Q formats

299   1187   1187  

galaxy

Data intensive science for everyone.

890   1129   1129  

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

92   1081   1081  

deep_gcns_torch

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arX...

157   1053   1053  

TDC

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Sc...

185   1053   1053  

react-plotly.js

A plotly.js React component from Plotly 📈

137   1042   1042  

MultiQC

Aggregate results from bioinformatics analyses across many samples int...

538   1027   1027  

rush

A cross-platform command-line tool for executing jobs in parallel

68   1026   1026  

cromwell

Scientific workflow engine designed for simplicity & scalability. Triv...

366   1017   1017  

adam

ADAM is a genomics analysis platform with specialized file formats bui...

311   1016   1016  

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

156   1004   1004  

scipipe

Robust, flexible and resource-efficient pipelines using Go and the com...

72   1003   1003  

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

304   931   931  

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

337   906   906  

hail

Cloud-native genomic dataframes and batch computing

228   885   885  

graphein

Protein Graph Library

109   856   856  

DeepPurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Func...

246   776   776  

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

168   773   773  

nucleus

Python and C++ code for reading and writing genomics data.

123   751   751  

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

117   730   730  

containers

Bioinformatics containers

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khmer

In-memory nucleotide sequence k-mer counting, filtering, graph travers...

311   717   717  

htslib

C library for high-throughput sequencing data formats

435   695   695  

seq

A high-performance, Pythonic language for bioinformatics

49   680   680  

wdl

Workflow Description Language - Specification and Implementations

300   666   666  

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification...

151   649   649  

biopandas

Working with molecular structures in pandas DataFrames

108   620   620  

bwa-mem2

The next version of bwa-mem

82   614   614  

jcvi

Python library to facilitate genome assembly, annotation, and comparat...

172   596   596  

dgl-lifesci

Python package for graph neural networks in chemistry and biology

135   593   593  

deepTools

Tools to process and analyze deep sequencing data.

200   582   582  

vsearch

Versatile open-source tool for microbiome analysis

121   578   578  

biostar-central

Biostar Q&A

231   553   553  

bioawk

BWK awk modified for biological data

116   552   552  

plantcv

Plant phenotyping with image analysis

244   548   548