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

Data intensive science for everyone.

Tools to process and analyze deep sequencing data.

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

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

A cool place to store your Hi-C

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

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

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

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

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

Extract 3D contacts (.pairs) from sequencing alignments

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Publication quality NGS track plotting

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

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

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 f…

Recentrifuge: robust comparative analysis and contamination removal for metagenomics