Explore projects
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Comparative genomics project of Ruminococcus gnavus, with additional prevalence and abundance analysis of worldwide metagenomic datasets.
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Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
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Generate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
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This repository gather all genomics data and analysis we performed on Zbtb24 in mouse embryonic stem cells.
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A Snakemake workflow to automatically handle metagenomics preprocessing (i.e. host removal and low-quality trimming).
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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
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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.
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A collection of semi-reusable scripts, which are not part of any official toolchain
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Repository containing a Snakemake ChIPseq pipeline for SE and PE datasets
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Functional metagenomics analysis using the HUMAnN tool version 3
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Use Kraken2 to quickly classify metagenomic reads and extract reads of taxa of interest to then assemble metagenomic assembled genomes (MAGs)
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