NeighborFinder is an R package enabling the identification of the local neighborhood of a species of interest, based on microbiome data.

CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data

A browser-based curation interface for contamination events detected by CroCoDeEL.

Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.

CroCoDeEL auxillary scripts and workflows

Workflow for quality control of FASTQ files, performing adapter removal, read trimming and host read removal

Workflow that randomly subsamples a fixed number of reads from FASTQ files

OneNet is a stability based network inference aggregation method from whole metagenome sequencing data, which aims at fostering reproducibility and precision

ESKRIM is a reference-free tool that compares microbial richness in shotgun metagenomic samples by counting k-mers