Most popular bioinformatics repositories and open source projects

signac

R toolkit for the analysis of single-cell chromatin data

81 238 238

wgsim

Reads simulator

88 237 237

parallel-fastq-dump

parallel fastq-dump wrapper

28 234 234

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

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

42 221 221

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

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

bigsnpr

R package for the analysis of massive SNP arrays.

44 200 200

AfterQC

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

52 197 197

SOAPdenovo2

Next generation sequencing reads de novo assembler.

76 193 193

pyfastx

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

17 192 192

circlator

A tool to circularize genome assemblies

49 192 192

drep

Rapid comparison and dereplication of genomes

33 191 191

MrBayes

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

73 191 191

tutorial

Tutorials on machine learning, artificial intelligence, data science w...

29 191 191

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

Workshop

课题组每周研讨会

50 188 188

splatter

Simple simulation of single-cell RNA sequencing data

53 188 188

bioc-refcard

Bioconductor cheat sheet

66 187 187

Plant-Disease-Identification-using-CNN

Plant Disease Identification Using Convulutional Neural Network

51 187 187

kent

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

82 187 187

bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with...

46 186 186

deepconsensus

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

35 185 185

krakenuniq

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

41 184 184

DRAM

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

41 184 184

dna2vec

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

60 183 183

genome-spy

A visualization grammar and GPU-accelerated toolkit for genomic data

11 183 183

lung_cancer_biomarker

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

0 183 183

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

63 180 180

amr

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

27 176 176

PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

40 174 174

scde

R package for analyzing single-cell RNA-seq data

66 173 173

gcp-for-bioinformatics

GCP for Bioinformatics Researchers

54 172 172

biograkn

BioGrakn Knowledge Graph

54 172 172

itol.toolkit

Helper Functions for Interactive Tree Of Life (iTOL)

17 172 172

genomics

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

50 171 171