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Screening contaminants for Illumina short reads-thanks to Dr Thanh Lee

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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

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

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Screening contaminants for Illumina short reads-thanks to Dr Thanh Lee

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  • Python 67.3%
  • Nextflow 32.7%