Cornet-2022-GBIO-Figshare.tgz (680.41 MB)
Download file

Software repository for Cornet and Baurain (2022) Contamination detection in genomic data: more is not enough

Download (680.41 MB)
posted on 2021-12-30, 13:53 authored by Luc CornetLuc Cornet, Denis BAURAINDenis BAURAIN
This repository provides Singularity definition files for six contamination detection tools. Database and files for Physeter are also provided, as well as the script to simulate the data.

- contams.def: Definition file for CheckM, Forty-Two, GUNC, Physeter and Kraken2
- eukcc.def: Definition file for EukCC
- life-tqmd-of73.dmnd: DIAMOND blast database for Physeter (from
- life-tqmd-of73.gca: List of GCA numbers for Physeter database (needed to enable the k-fold mode)
- contam-labels.idl: idl file use for Physeter and Forty-Two (from
- taxdump-20211206: NCBI Taxonomy dump used across the study
- Python script used to create the chimeric bacterial genome


BELSPO - Belgian Science Policy Office (grant no. B2/191/P2/BCCM GEN-ERA)