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

Official code repository for GATK versions 4 and up

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

Data intensive science for everyone.

Tools to process and analyze deep sequencing data.

Java utilities for Bioinformatics

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

Customizable workflows based on snakemake and python for the analysis of NGS data

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

A collection of Galaxy-related training material

RNA-seq workflow using STAR and DESeq2

Tools for working with genomic and high throughput sequencing data.

R package for analyzing single-cell RNA-seq data

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Detect and visualize target mutations by scanning FastQ files directly

UGENE is free open-source cross-platform bioinformatics software

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

Sequana: a set of Snakemake NGS pipelines

R package for analyzing and interactively exploring large single-cell RNA-seq datasets

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

Rare variant test software for next generation sequencing data

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Cloud agnostic genomics analysis, scientific computation and storage platform

Generate consensus reads to reduce sequencing noises and remove duplications

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

A method for variant graph genotyping based on exact alignment of k-mers

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.