Cleaning FASTQ files containing a contamination sequence.
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5.6 years ago

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.

fastq • 2.1k views
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5.6 years ago
GenoMax 115k

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

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5.6 years ago
lexnederbragt ★ 1.3k

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

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