Top 704 bioinformatics open source projects

Structural variation caller using third generation sequencing

Haplotype VCF comparison tools

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

A curated list of Cheminformatics libraries and software.

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

Core BioPerl 1.x code

cython + htslib == fast VCF and BCF processing

Strelka2 germline and somatic small variant caller

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Quickly search, compare, and analyze genomic and metagenomic data sets.

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Examples of using deep learning in Bioinformatics

Remote protein homology detection suite.

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

An ultrafast memory-efficient short read aligner

🔬 Assemble large genomes using short reads

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

React component for Cytoscape.js network visualisations

🔬 BEDOPS: high-performance genomic feature operations

A curated list of resources for learning bioinformatics.

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Proof-of-concept seq-to-graph mapper and graph generator

code for reading and processing Allen Institute for Brain Science data

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

Python package for graph neural networks in chemistry and biology

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

RAxML Next Generation: faster, easier-to-use and more flexible

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Protein Graph Library

Deep learning infrastructure for bioinformatics

Python for Bioinformatics

Toolset for SV simulation, comparison and filtering

Ten Quick Tips for Deep Learning in Biology

Reads simulator

Genome assembly evaluation tool

Rapid large-scale prokaryote pan genome analysis

Cuneiform distributed programming language

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Curated (meta)list of resources for Biology.

Annotated data.

A repository for setting up a RNAseq workflow

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Tools for working with genomic and high throughput sequencing data.

Syntax highlighting for computational biology

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

The sources of the openSNP website

Bioconductor cheat sheet

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

BioGrakn Knowledge Graph

Next generation sequencing reads de novo assembler.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

R package for analyzing single-cell RNA-seq data

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Package for fetching metadata and downloading data from SRA/ENA/GEO

A curated list of bioinformatics bench-marking papers and resources.