Most popular bioinformatics repositories and open source projects

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

42 221 221

bioSyntax

Syntax highlighting for computational biology

31 217 217

bioinf-python

Python for Bioinformatics

106 216 216

cuneiform

Cuneiform distributed programming language

15 215 215

weekly

生信爱好者周刊（每周日发布）

19 213 213

hgvs

Python library to parse, format, validate, normalize, and map sequence...

85 212 212

Blacklist

Application for making ENCODE Blacklists

32 212 212

pronto

A Python frontend to (Open Biomedical) Ontologies.

42 211 211

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "l...

31 204 204

DeepECG

ECG classification programs based on ML/DL methods

81 204 204

snp-sites

Finds SNP sites from a multi-FASTA alignment file

47 202 202

masurca

34 202 202

scgen

Single cell perturbation prediction

45 202 202

goleft

goleft is a collection of bioinformatics tools distributed under MIT l...

24 201 201

Artemis

Artemis is a free genome viewer and annotation tool that allows visual...

73 200 200

AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for...

52 197 197

SOAPdenovo2

Next generation sequencing reads de novo assembler.

76 193 193

circlator

A tool to circularize genome assemblies

49 192 192

pyfastx

a python package for fast random access to sequences from plain and gz...

17 192 192

MrBayes

MrBayes is a program for Bayesian inference and model choice across a...

73 191 191

drep

Rapid comparison and dereplication of genomes

33 191 191

tools

Python package with helper tools for the nf-core community.

142 190 190

HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, nor...

68 189 189

splatter

Simple simulation of single-cell RNA sequencing data

53 188 188

kent

UCSC Genome Browser source tree. Stable branch: "beta".

82 187 187

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors i...

35 185 185

krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for m...

41 184 184

DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotat...

41 184 184

lung_cancer_biomarker

Bioinformatics Project. Trying to find out the most influential metabo...

0 183 183

lightdock

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

25 182 182

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

63 180 180

bioc-refcard

Bioconductor cheat sheet

62 179 179

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence...

27 176 176

PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

40 174 174

ugene

UGENE is free open-source cross-platform bioinformatics software

54 173 173

biograkn

BioGrakn Knowledge Graph

54 172 172

gcp-for-bioinformatics

GCP for Bioinformatics Researchers

54 172 172

genomics

A collection of scripts and notes related to genomics and bioinformati...

50 171 171

Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for varia...

26 169 169

DnaChisel

:pencil2: A versatile DNA sequence optimizer

32 169 169

PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

20 168 168

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

19 167 167

pyani

Application and Python module for average nucleotide identity analyses...

55 166 166

snpr

The sources of the openSNP website

46 164 164

scde

R package for analyzing single-cell RNA-seq data

66 164 164

biofast

Benchmarking programming languages/implementations for common tasks in...

26 164 164

smudgeplot

Inference of ploidy and heterozygosity structure using whole genome se...

20 164 164

RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://githu...

28 163 163

dna2vec

dna2vec: Consistent vector representations of variable-length k-mers

60 162 162

cooler

A cool place to store your Hi-C

49 162 162