Cleaning FASTQ files containing a contamination sequence.
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.
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lexnederbragt
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Pierre Lindenbaum
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Pierre Lindenbaum
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I recently discovered AdapterRemoval https://github.com/MikkelSchubert/adapterremoval, give it a try.
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