Structural variation caller using third generation sequencing
Haplotype VCF comparison tools
Official git repository for Biopython (originally converted from CVS)
cython + htslib == fast VCF and BCF processing
Strelka2 germline and somatic small variant caller
Quickly search, compare, and analyze genomic and metagenomic data sets.
🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
Remote protein homology detection suite.
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)
🔬 BEDOPS: high-performance genomic feature operations
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
A genome browser that shows long reads and complex variants better
Deep learning infrastructure for bioinformatics
Toolset for SV simulation, comparison and filtering
Ten Quick Tips for Deep Learning in Biology
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
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
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
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