Explore projects

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

This repository gather all genomics data and analysis we performed on Zbtb24 in mouse embryonic stem cells.

Mirror of https://github.com/LOVDnl/LOVD3.git

Website and materials for our Git courses

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.

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

Repository for Jianhui's snakemake pipeline

Repository containing a Snakemake ChIPseq pipeline for SE and PE datasets

Functional metagenomics analysis using the HUMAnN tool version 3

Generate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes

Use Kraken2 to quickly classify metagenomic reads and extract reads of taxa of interest to then assemble metagenomic assembled genomes (MAGs)

An automated workflow for taxonomically classifying assembled scaffolds from metagenomics data.

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

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

Screen fecal metagenomes of polyposis patients for the presence of the pks gene island of procarcinogenic E. coli

Template for SASC projects