Exclude reads with specific adapters #2
Description
Thanks for writing this - I'm currently testing methods for adapter filtering in our HiFi reads and this is giving some nice results!
I was wondering if there would be scope for a feature for a set of "exclude" adapters, where any read matching a given sequence (either at the ends, in the middle, or both, depending on the sequence) can be dropped? We are doing multiplexed runs and sometimes we see reads with barcodes for other samples appear in the read set - I would like to drop these entirely from the output rather than trim the ends as there's a chance the read belongs to a different sequencing library. (edit: maybe adapter-specific trim/discard options, enumerated in the fasta headers, might be a good option?)
Also, it would be nice if the tool could output a list of reads which were affected, what happened to them (trimmed or discarded), and for which adapter(s), for QC purposes.