Adapter Schemes
CutSeq bundles built-in library schemes — list them in a terminal with cutseq --list-adapters, and use a name (or a custom grammar string) via -A/--adapter-scheme (-a is an alias).
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Inline-barcode auto-detection
Inline barcodes are written in lowercase (acgt...). If you write one in uppercase, it merges with the adjacent sequencing primer into one adapter run. CutSeq checks the two outermost adapters of a scheme against a curated database of Illumina / BGI (MGI) sequencing primers (cutseq --list-primers) and reclassifies any fixed uppercase sequence adjacent to (or between) recognized primers as an inline barcode, with a warning. Custom schemes without known primers are never altered. Disable with --no-auto-inline.
Discarding reads with a reason tag
A single -d output collects every rejected read with the reason in the name (reason=too_short, reason=too_many_n, reason=low_quality, reason=no_barcode), gated by -m/--min-length, --max-n, --min-avg-quality and --ensure-inline-barcode. When no -d/-O is given, discard files are auto-named from the inputs.