cocoremover 0.1.2

Cocoremover is a simple tool for the removal of contaminant contigs from bacterial genome assemblies.

How to use 🎬

1. Build a fresh, updated reference database (eg using 36 cores):

   cocoremover -c 36 --makedb

2. Run the decontamination of a genome (eg using 36 cores):

   cocoremover -c 36 -i GCA_948938835.1.fna -t 1598 -d cocoremover.db

The required parameter -t/--taxid is the species-level NCBI Taxonomy ID for the input genome assembly. Please use cocoremover --help to read the full user guide.

Output files will be created:

• {assembly}.counts: shows, for each contig, the number of genes for each detected species. If the species with the highest number of genes is different from the one specified with --taxid, then the contig is assumed as contaminant.
• {assembly}.CT.{ext}: FASTA file containing contigs marked as contaminant.
• {assembly}.OK.{ext}: original genome assembly with the contaminating contigs removed.

How to install ⚙️

pip install cocoremover

Cocoremover has several dependencies that need to be satisfied beforehand. They are all easily installable through conda/mamba. If dependencies are not found at the startup, the user will be notified.

• diamond: GitHub - Paper - conda
• esearch, esummary, xtract: Link - conda
• wget: conda
• tar: conda
• parallel: Link - conda
• prodigal: GitHub - Paper - conda
• gzip: conda

How to cite ✍🏼

Lazzari G., Felis G. E., Salvetti E., Calgaro M., Di Cesare F., Teusink B., Vitulo N. Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models. mSystems. December 2025. https://doi.org/10.1128/msystems.01007-25

If you use this tool in your work, remember to specify its version.