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.

C library for high-throughput sequencing data formats

Tools to process and analyze deep sequencing data.

Java utilities for Bioinformatics

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

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

A collection of Galaxy-related training material

Tools for working with genomic and high throughput sequencing data.

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

R package for analyzing single-cell RNA-seq data

UGENE is free open-source cross-platform bioinformatics software

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

Detect and visualize target mutations by scanning FastQ files directly

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

Rare variant test software for next generation sequencing data

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

Cloud agnostic genomics analysis, scientific computation and storage platform

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.

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

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

Generate consensus reads to reduce sequencing noises and remove duplications

Annotation and Ranking of Structural Variation

GATK RNA-Seq Variant Calling in Nextflow