Benjamin Guinet

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

metaJAM: a Nextflow integrated metagenomic workflow for sedimentary ancient DNA

metaJAM provides a scalable, user-friendly Nextflow pipeline for metagenomic ancient DNA analysis, improving taxonomic accuracy and workflow flexibility.

AncientMetagenomeDir dating metadataset highlights need for standardised radiocarbon reporting in ancient DNA

The paper adds standardized radiocarbon dating information to the AncientMetagenomeDir dataset, highlighting inconsistencies in radiocarbon reporting across ancient metagenomic studies.

The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts

This study shows that reference genome divergence reduces the detectability of aDNA damage patterns in metagenomic data and introduces a correction method to improve damage signal recovery.

Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data

The paper presents a method to identify and mask microbial-like sequences in eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data.

Dating the origin of a viral domestication event in parasitoid wasps attacking Diptera

This study identifies 18 viral genes endogenized in 41 Cynipoidea wasps around 75 million years ago, linking viral domestication to wasp diversification.

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

The paper investigates the link between endoparasitoid lifestyle and the endogenization and domestication of dsDNA viruses in Hymenoptera genomes.