Cleaning FASTQ files containing a contamination sequence.

Question

[Pierre Lindenbaum]

Using the technology [censored] we have found a sequence (n = ~80bp) which look like a contaminant in our 2x150 fastq files.

I would like to trim the whole sequence of the reads containing some significative parts of this contaminant.

What would be the best tool to achieve this ? cutadapt ? whith which params ?

Thanks,

P.

Answer 1

[GenoMax]

bbduk.sh from BBMap with literal=your_contaminant_seq option. Significant part is how many bases? Many other options for bbduk to play with.

Answer 2

[lexnederbragt]

I recently discovered AdapterRemoval https://github.com/MikkelSchubert/adapterremoval, give it a try.