Fastp

Question

[akis]

Hi,

Does anyone know if the fastp tool can detect adapters solely from a library, or can it also identify unknown adapters?

Answer 1

[Juke34]

Yes FASTP can detect unknown adapters. See README

# adapters

Adapter trimming is enabled by default, but you can disable it by -A or --disable_adapter_trimming. Adapter sequences can be automatically detected for both PE/SE data.

For SE data, the adapters are evaluated by analyzing the tails of first ~1M reads. This evaluation may be inacurrate, and you can specify the adapter sequence by -a or --adapter_sequence option. If adapter sequence is specified, the auto detection for SE data will be disabled.

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[akis]

Thank you very much for your answer.