AKA: how to remove contamination from your metagenome! We use sharks genomes, but it works with humans, corals, and other things too!

A while ago we wrote deconseq to allow you to remove contamination from your sequence libraries. We used an HTS-mapper to map the reads in your sequences to your reference genome, and then filtered the sequences after mapping.

This is trivial to do with modern sequence analysis tools, and so we provide recipes here for filtering your reads based on matches to a reference genome. Read more to find out how!

We also provide a snakefile that does all these steps. Set up the bowtie2 index, a directory of reads, and and output location, and it will generate mapped and unmapped reads for you!

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