Explore projects

A Snakemake workflow to automatically handle metagenomics preprocessing (i.e. host removal and low-quality trimming).

Pipeline to pre-process vcf and gvcf files and submit them to varda.lumc.nl

RNA-seq pipeline for AML diagnostics. Illustration from Anatomy & Physiology, licenced under the Creative Commons Attribution 3.0 Unported

This is the user guide for the Shark CentOS-8 Slurm-20.02 cluster. This will give the user a short introduction to the cluster and how to use it.

Analyses of antimicrobial resistance genes in metagenomic data from patients with (multiple) recurrent Clostridioides difficile infections and their faecal microbiota transplantation donors - with culture data from multidrug resistant organisms

Snakemake-based WES/IDP pipeline for LDGA.

Automated and parallelised workflow to assemble PacBio HiFi reads of bacteria whole-genome sequencing. Also subsamples reads before assembly and re-orients resulting contigs to the 'correct' starting position.

Mirror of https://github.com/mutalyzer/backtranslate.git

Engraftment calculations based on One Codex species-level taxonomic classifications of shotgun metagenomic read sets of the FECBUD trial - a collaboration between the Netherlands Donor Feces Bank and Vedanta Biosciences.

A collection of semi-reusable scripts, which are not part of any official toolchain