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hariszaf / pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
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Enhancement: Add option for users to provide a custom adapter file #40

Open natgiot opened 2 years ago

natgiot commented 2 years ago

It is very common that NGS data contain adapter sequences other than the ones used during library construction, mainly because sequencing centers may sequence many different libraries at the same time. This cross-contamination, and any other project-specific contamination of reads with short sequences, can be handled easily if the user has the option to provide a custom adapter file in PEMA. Thank you for considering!

hariszaf commented 2 years ago

This can be done by enabling the fastaWithAdaptersEtc parameter of Trimmomatic; see page 6. I will implement this for the next pema version.