Most popular bioinformatics repositories and open source projects

bioconvert

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

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Bismark

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

98   322   322  

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework bas...

45   321   321  

strelka

Strelka2 germline and somatic small variant caller

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bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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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  

canvasXpress

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

44   294   294  

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

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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 Informatio...

29   266   266  

Roary

Rapid large-scale prokaryote pan genome analysis

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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  

intermine

A powerful open source data warehouse system

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histolab

Library for Digital Pathology Image Processing

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sarek

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

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sequenceserver

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

112   253   253  

DeepECG

ECG classification programs based on ML/DL methods

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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 Exploratio...

55   247   247  

cellrank

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

28   246   246  

bowtie

An ultrafast memory-efficient short read aligner

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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

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kaiju

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

63   230   230  

truvari

Structural variant toolkit for VCFs

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