Explore projects

An automated workflow for generating metagenomic assemblies with a focus on reconstructing plasmids.

A pipeline to automatically screen the output by Jovian for the presence of species and sequences (genes) of interest, and quantify them.

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

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

Practica files for the workshop

Rig framework pipeline -- magpie

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

Time-analysis module for DRMAA-based snakemake runs

Data analysis tools for Next Generation Sequencing of forensic DNA markers, including tools for characterisation and filtering of PCR stutter artefacts and other systemic noise, and for automatic detection of the alleles in a sample.

Library implementing Generalized Enhanched Suffix Arrays (GESAs)

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.

Analysis scripts used to analyse the procarcinogenic pks gene island in metagenomes of multiple recurrent Clostridioides difficile infected patients and their corresponding healthy donors from the Netherlands Donor Feces Bank.

Data analysis skeleton.

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