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Thanks @colinbrislawn! I transferred this issue over to q2-types, since the problem is actually with the format, and not with q2-cutadapt (cutadapt doesn't look at the quality scores when doing nucleotide pattern matching, which is all that we have exposed in q2-cutadapt at present). I think supporting a PHRED64 variant of the formats listed above would make sense, and would probably work similarly to how the PHRED64 manifests work (by converting PHRED offset on import).
Improvement Description
Allow users to import a PHRED 64 variant of the
MultiplexedSingleEndBarcodeInSequence
/MultiplexedSPairedEndBarcodeInSequence
.References
form xpost
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