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Top 577 bioinformatics open source projects

Sniffles
Structural variation caller using third generation sequencing
Hap.py
Haplotype VCF comparison tools
Dash.jl
Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.
Awesome Cheminformatics
A curated list of Cheminformatics libraries and software.
Bioperl Live
Core BioPerl 1.x code
Cyvcf2
cython + htslib == fast VCF and BCF processing
Strelka
Strelka2 germline and somatic small variant caller
Single Cell Pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
Sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
Homebrew Bio
🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
Deep learning examples
Examples of using deep learning in Bioinformatics
Hh Suite
Remote protein homology detection suite.
Bowtie
An ultrafast memory-efficient short read aligner
Abyss
🔬 Assemble large genomes using short reads
Miniasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
React Cytoscapejs
React component for Cytoscape.js network visualisations
Bedops
🔬 BEDOPS: high-performance genomic feature operations
Awosome Bioinformatics
A curated list of resources for learning bioinformatics.
Awesome Cancer Variant Databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Minigraph
Proof-of-concept seq-to-graph mapper and graph generator
Allensdk
code for reading and processing Allen Institute for Brain Science data
Sequenceserver
Intuitive local web frontend for the BLAST bioinformatics tool
Dgl Lifesci
Python package for graph neural networks in chemistry and biology
Deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Raxml Ng
RAxML Next Generation: faster, easier-to-use and more flexible
Seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Karyoploter
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Ribbon
A genome browser that shows long reads and complex variants better
Janggu
Deep learning infrastructure for bioinformatics
Bioinf Python
Python for Bioinformatics
Survivor
Toolset for SV simulation, comparison and filtering
Wgsim
Reads simulator
Quast
Genome assembly evaluation tool
Roary
Rapid large-scale prokaryote pan genome analysis
Goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Awesome Biology
Curated (meta)list of resources for Biology.
Rnaseq Workflow
A repository for setting up a RNAseq workflow
Afterqc
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Fgbio
Tools for working with genomic and high throughput sequencing data.
Biosyntax
Syntax highlighting for computational biology
Ragoo
Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag
Snpr
The sources of the openSNP website
Bioc Refcard
Bioconductor cheat sheet
Clairvoyante
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Biograkn
BioGrakn Knowledge Graph
Soapdenovo2
Next generation sequencing reads de novo assembler.
Mixcr
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.
Scde
R package for analyzing single-cell RNA-seq data
Kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
Awesome Bioinformatics Benchmarks
A curated list of bioinformatics bench-marking papers and resources.
1-60 of 577 bioinformatics projects