Most popular bioinformatics repositories and open source projects

bioconvert

Bioconvert is a collaborative project to facilitate the interconversio...

41   322   322  

Bismark

A tool to map bisulfite converted sequence reads and determine cytosin...

98   322   322  

strelka

Strelka2 germline and somatic small variant caller

103   320   320  

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

33   319   319  

quast

Genome assembly evaluation tool

71   317   317  

raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

55   312   312  

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covale...

95   309   309  

bionode

Modular and universal bioinformatics

41   302   302  

pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes:...

50   297   297  

AllenSDK

code for reading and processing Allen Institute for Brain Science data

141   297   297  

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package ma...

120   285   285  

octopus

Bayesian haplotype-based mutation calling

36   285   285  

bioperl-live

Core BioPerl 1.x code

179   283   283  

awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases a...

63   282   282  

awesome-biology

Curated (meta)list of resources for Biology.

44   281   281  

SURVIVOR

Toolset for SV simulation, comparison and filtering

42   280   280  

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

102   278   278  

fgbio

Tools for working with genomic and high throughput sequencing data.

60   277   277  

abyss

:microscope: Assemble large genomes using short reads

99   276   276  

canvasXpress

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit...

42   274   274  

bedops

:microscope: BEDOPS: high-performance genomic feature operations

57   272   272  

miniasm

Ultrafast de novo assembly for long noisy reads (though having no cons...

67   272   272  

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creatin...

25   269   269  

awesome-bioie

🧫 A curated list of resources relevant to doing Biomedical Information...

29   266   266  

Roary

Rapid large-scale prokaryote pan genome analysis

186   265   265  

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation...

77   265   265  

GLUE

Graph-linked unified embedding for single-cell multi-omics data integr...

39   264   264  

karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along t...

37   263   263  

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

46   260   260  

Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure f...

64   257   257  

histolab

Library for Digital Pathology Image Processing

48   256   256  

sarek

Analysis pipeline to detect germline or somatic variants (pre-processi...

307   254   254  

sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics too...

112   253   253  

genometools

GenomeTools genome analysis system.

60   251   251  

awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

50   251   251  

immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration...

55   247   247  

cellrank

CellRank: dynamics from multi-view single-cell data. See the docs:

28   246   246  

intermine

A powerful open source data warehouse system

354   244   244  

bowtie

An ultrafast memory-efficient short read aligner

76   242   242  

janggu

Deep learning infrastructure for genomics

30   241   241  

Ribbon

A genome browser that shows long reads and complex variants better

30   239   239  

signac

R toolkit for the analysis of single-cell chromatin data

81   238   238  

wgsim

Reads simulator

88   237   237  

dance

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell...

20   236   236  

parallel-fastq-dump

parallel fastq-dump wrapper

28   234   234  

serratus

Ultra-deep search for novel viruses

31   232   232  

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a...

63   230   230  

truvari

Structural variant toolkit for VCFs

40   230   230  

deep-rules

Ten Quick Tips for Deep Learning in Biology

48   224   224  

miniprot

Align proteins to genomes with splicing and frameshift

10   224   224