Most popular bioinformatics repositories and open source projects

cs-video-courses

List of Computer Science courses with video lectures.

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dash

Data Apps & Dashboards for Python. No JavaScript Required.

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biopython

Official git repository for Biopython (originally converted from CVS)

1634   3665   3665  

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

629   3331   3331  

deepvariant

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

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awesome-single-cell

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

852   2566   2566  

nextflow

A DSL for data-driven computational pipelines

547   2081   2081  

fastp

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

302   1541   1541  

scanpy

Single-cell analysis in Python. Scales to >1M cells.

511   1515   1515  

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  

bwa

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

538   1319   1319  

seqtk

Toolkit for processing sequences in FASTA/Q formats

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galaxy

Data intensive science for everyone.

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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  

seqkit

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

145   1038   1038  

MultiQC

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

538   1027   1027  

adam

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

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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  

cromwell

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

334   903   903  

hail

Cloud-native genomic dataframes and batch computing

228   885   885  

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

333   873   873  

csvtk

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

82   859   859  

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  

rush

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

59   724   724  

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  

containers

Bioinformatics containers

213   589   589  

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

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bioawk

BWK awk modified for biological data

116   552   552  

plantcv

Plant phenotyping with image analysis

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