Most popular bioinformatics repositories and open source projects

alphapept

A modular, python-based framework for mass spectrometry. Powered by nb...

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blasr

BLASR: The PacBio® long read aligner

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psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC...

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pydna

Clone with Python! Data structures for double stranded DNA & simulatio...

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dockstore

An app store for scientific workflows, tools, notebooks, and services

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OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Regi...

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mag

Assembly and binning of metagenomes

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MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

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rasusa

Randomly subsample sequencing reads to a specified coverage

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metaGEM

:gem: An easy-to-use workflow for generating context specific genome-s...

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harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and...

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SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signature...

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weblogo

WebLogo 3: Sequence Logos redrawn

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VariantSpark

machine learning for genomic variants

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Multi-BioNER

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Le...

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apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation

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fqtools

An efficient FASTQ manipulation suite

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lineage

tools for genetic genealogy and the analysis of consumer DNA test resu...

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souporcell

Clustering scRNAseq by genotypes

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rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimi...

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SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

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seq2science

Automated and customizable preprocessing of Next-Generation Sequencing...

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Terpene-Profile-Parser-for-Cannabis-Strains

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

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gencore

Generate duplex/single consensus reads to reduce sequencing noises and...

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gatk-sv

A structural variation pipeline for short-read sequencing

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pandora

:chart: PANDORA: Revolutionizing Biomedical Research with Advanced Mac...

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GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

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decontam

Simple statistical identification and removal of contaminants in marke...

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pybel

🌶️ An ecosystem in Python for working with the Biological Expression L...

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ccs

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

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Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural...

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tskit

Population-scale genomics

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gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial...

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sage

Proteomics search & quantification so fast that it feels like magic

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BuddySuite

Bioinformatics toolkits for manipulating sequence, alignment, and phyl...

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bio4j

Bio4j abstract model and general entry point to the project

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peddy

genotype :: ped correspondence check, ancestry check, sex check. direc...

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snakefmt

The uncompromising Snakemake code formatter

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muscle

Multiple sequence alignment with top benchmark scores scalable to thou...

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FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein seq...

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atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (pr...

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vdjdb-db

🗂️ Git-based TCR database storage & management. Submissions welcome!

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bedtk

A simple toolset for BED files (warning: CLI may change before bedtk b...

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ksw2

Global alignment and alignment extension

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DNAnalyzer

Revolutionizing DNA analysis and making it accessible to all through i...

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kana

Single cell analysis in the browser

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vdjtools

Post-analysis of immune repertoire sequencing data

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svtyper

Bayesian genotyper for structural variants

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CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

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cLoops

Accurate and flexible loops calling tool for 3D genomic data.

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