Most popular bioinformatics repositories and open source projects

rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulation...

39   111   111  

RaPDTool

Rapid Profiling and Deconvolution Tool for Metagenomes

87   110   110  

ontobio

python library for working with ontologies and ontology associations

31   109   109  

globalbioticinteractions

Global Biotic Interactions provides access to existing species interac...

15   109   109  

plant-seg

A tool for cell instance aware segmentation in densely packed 3D volu...

34   108   108  

FastQt

FastQC port to Qt5: A quality control tool for high throughput sequenc...

25   108   108  

arv

A fast 23andMe DNA parser and inferrer for Python

5   108   108  

V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral ge...

34   108   108  

bionitio

Demonstrating best practices for bioinformatics command line tools

24   107   107  

dockstore

Our VM/Docker sharing infrastructure and management component

28   107   107  

GeneFuse

Gene fusion detection and visualization

57   107   107  

RNAlysis

RNA sequencing analysis software

13   107   107  

spacegraphcats

Indexing & querying large assembly graphs -- in space, no one can hear...

14   106   106  

plass

Protein-Level ASSembler (PLASS): sensitive and precise protein assembl...

11   106   106  

UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena plat...

12   106   106  

fermikit

De novo assembly based variant calling pipeline for Illumina short rea...

23   105   105  

saber

Saber is a deep-learning based tool for information extraction in the...

17   105   105  

swarm

A robust and fast clustering method for amplicon-based studies

21   105   105  

dbsnp

dbSNP

48   105   105  

biocypher

A unifying framework for biomedical research knowledge graphs

14   105   105  

mygene.info

MyGene.info: A BioThings API for gene annotations

21   104   104  

biojava-tutorial

:book::books:An introductory tutorial for BioJava

40   104   104  

SNPRelate

R package: parallel computing toolset for relatedness and principal co...

25   104   104  

fastqp

Simple FASTQ quality assessment using Python

16   103   103  

molgenis

MOLGENIS - for scientific data: management, exploration, integration a...

101   103   103  

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes...

23   103   103  

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via...

27   102   102  

Clair

Clair: Exploring the limit of using deep neural network on pileup data...

12   102   102  

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, traine...

25   102   102  

swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visuali...

21   101   101  

BioFSharp

Open source bioinformatics and computational biology toolbox written i...

33   101   101  

dolphinnext

A graphical user interface for distributed data processing of high thr...

22   101   101  

nightingale

Data visualisation web components for the life sciences.

29   100   100  

hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common...

21   100   100  

DEEPScreen

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks...

34   99   99  

perbase

Per-base per-nucleotide depth analysis

12   99   99  

deepsignal

Detecting methylation using signal-level features from Nanopore sequen...

20   99   99  

best

Bam Error Stats Tool (best): analysis of error types in aligned reads.

5   99   99  

strobealign

Aligns short reads using dynamic seed size with strobemers

13   98   98  

GenomicsDB

High performance data storage for importing, querying and transforming...

16   98   98  

grabseqs

A utility for easy downloading of reads from next-gen sequencing repos...

14   98   98  

GenomicConsensus

PacBio® variant and consensus caller

43   98   98  

ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED...

91   98   98  

block-aligner

SIMD-accelerated library for computing global and X-drop affine gap pe...

6   98   98  

NucleoATAC

nucleosome calling using ATAC-seq

29   97   97  

Terpene-Profile-Parser-for-Cannabis-Strains

Parser and database to index the terpene profile of different strains...

20   97   97  

chewBBACA

BSR-Based Allele Calling Algorithm

23   97   97  

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for ge...

3   96   96  

cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleo...

4   96   96  

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipelin...

69   96   96