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

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

software

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.

Singularity

- contams.def: Definition file for CheckM, Forty-Two, GUNC, Physeter and Kraken2

- eukcc.def: Definition file for EukCC

Physeter

- life-tqmd-of73.dmnd: DIAMOND blast database for Physeter (from https://doi.org/10.3389/fmicb.2021.755101)

- 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 https://bitbucket.org/phylogeno/42-ribo-msas/)

- taxdump-20211206: NCBI Taxonomy dump used across the study

Simulations

- Chimeric-genomes.py: Python script used to create the chimeric bacterial genome

Funding

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

History

Usage metrics

Keywords

Contamination detection Bioinformatics software Singularity container technology NCBI Taxonomy Bacteriology Bioinformatics Computational Biology Genomics Microbial Ecology Microbiology Phylogeny and Comparative Analysis

Licence

CC BY 4.0