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)

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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...

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Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

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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.

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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  

seqkit

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

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MultiQC

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

538   1027   1027  

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  

adam

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

307   953   953  

react-plotly.js

A plotly.js React component from Plotly 📈

135   935   935  

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  

csvtk

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

82   859   859  

graphein

Protein Graph Library

109   856   856  

TDC

Therapeutics Data Commons: Artificial Intelligence Foundation for Ther...

146   830   830  

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  

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

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seq

A high-performance, Pythonic language for bioinformatics

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wdl

Workflow Description Language - Specification and Implementations

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salmon

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

151   649   649  

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

291   642   642  

Simple-GPU

🦒 Functional WebGPU

3   622   622  

biopandas

Working with molecular structures in pandas DataFrames

108   620   620  

bwa-mem2

The next version of bwa-mem

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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  

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

96   556   556  

biostar-central

Biostar Q&A

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bioawk

BWK awk modified for biological data

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