Most popular bioinformatics repositories and open source projects

RNArtist

RNArtist allows you to design and paint your RNA 2D structures interac...

9   95   95  

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Re...

31   94   94  

kalign

A fast multiple sequence alignment program.

26   94   94  

fastq.bio

An interactive web tool for quality control of DNA sequencing data

12   93   93  

bcalm

compacted de Bruijn graph construction in low memory

20   93   93  

assembly-stats

Get assembly statistics from FASTA and FASTQ files

22   93   93  

python_biologist

Python Programming for Biologists

72   93   93  

owltools

OWLTools

30   92   92  

HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from...

30   92   92  

reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the i...

26   92   92  

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled org...

33   92   92  

CAFE

Analyze changes in gene family size and provide a statistical foundati...

36   91   91  

awesome-genetics

A curated list of awesome bioinformatics software.

5   91   91  

BWA-MEME

BWA-MEME: Faster BWA-MEM2 using learned-index

13   91   91  

af2complex

Predicting direct protein-protein interactions with AlphaFold deep lea...

15   90   90  

bio_scripts

Practical, reusable scripts for bioinformatics

64   90   90  

What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

15   90   90  

yak

Yet another k-mer analyzer

3   90   90  

cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

12   89   89  

gramtools

Genome inference from a population reference graph

14   89   89  

open-cravat

A modular annotation tool for genomic variants

19   89   89  

smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config

13   89   89  

RIDDLE

Race and ethnicity Imputation from Disease history with Deep LEarning

16   88   88  

biomake

GNU-Make-like utility for managing builds and complex workflows

9   88   88  

freesasa

C-library for calculating Solvent Accessible Surface Areas

34   88   88  

bgt

Flexible genotype query among 30,000+ samples whole-genome

9   87   87  

goenrich

GO enrichment with python -- pandas meets networkx

24   87   87  

havengrc

☁️Haven GRC - easier governance, risk, and compliance 👨‍⚕️👮‍♀️🦸‍♀️🕵...

20   87   87  

rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Packag...

21   87   87  

platon

Identification & characterization of bacterial plasmid-borne contigs f...

15   86   86  

foldcomp

Compressing protein structures effectively with torsion angles

8   86   86  

TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a no...

17   85   85  

wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genom...

19   85   85  

decoupler-py

Python package to infer biological activities from omics data using a...

12   85   85  

CharGer

Characterization of Germline variants

38   85   85  

arcs

🌈Scaffold genome sequence assemblies using linked or long read sequen...

15   85   85  

snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows (STAR an...

37   85   85  

referenceseeker

Rapid determination of appropriate reference genomes.

5   85   85  

QUBEKit

Quantum Mechanical Bespoke Force Field Derivation Toolkit

26   85   85  

hickit

TAD calling, phase imputation, 3D modeling and more for diploid single...

11   84   84  

minced

Mining CRISPRs in Environmental Datasets

15   84   84  

PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation N...

27   84   84  

skani

Fast, robust ANI and aligned fraction for metagenomic genomes and cont...

4   83   83  

awesome-10x-genomics

List of tools and resources related to the 10x Genomics GEMCode/Chromi...

15   83   83  

bget

Portable command-line tool to query bioinformatics APIs, data, databas...

17   83   83  

flo

Same species annotation lift over pipeline.

26   83   83  

PyFeat

A Python-based Effective Feature Generation Tool from DNA, RNA, and Pr...

26   83   83  

STARTapp

The START App: R Shiny Transcriptome Analysis Resource Tool

40   82   82  

dammit

just annotate it, dammit!

25   82   82  

flowr

Robust and efficient workflows using a simple language agnostic approa...

10   82   82