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

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

SPAdes Genome Assembler

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Simple & Efficient data access for Scala and Scala.js

A repository for setting up a RNAseq workflow

A Python package for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom actions.

Structural variant toolkit for VCFs

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Rapid large-scale prokaryote pan genome analysis

A minimal and human-readable language and environment for the live coding of algorithmic electronic music.

Analysis Pipeline for Single Cell ATAC-seq

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

A Java API for high-throughput sequencing data (HTS) formats.

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

SortMeRNA: next-generation sequence filtering and alignment tool

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

Finds SNP sites from a multi-FASTA alignment file

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

UGENE is free open-source cross-platform bioinformatics software

A tool to circularize genome assemblies

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

A collection of scripts and notes related to genomics and bioinformatics

:rocket: A sequencing simulator

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins