A small nextflow script for screening contaminants from Illumina short reads and estimate bacterial genome size

It uses centrifuge for reads classification; some options (kmc, bbtools, mash) for estimation of genome size.

Dependencies:

All the tools can be installed via bioconda

- centrifuge
- mash
- krona
- kmc
- bbtools

• Centrifuge database and Krona taxonomy: https://genomics.sschmeier.com/downloads.html#downloads

• Mash RefSketch database: https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh

How to run:

• Edit location to the centrifuge database and Mash
• Edit pattern of reads if needed

nextflow run speciation.nf --input /path/to/folder/of/reads --output /path/to/folder/of/results