✂️ CutSeq

Why CutSeq?

NGS library prep can need many sequential trimming and extraction steps. The SMARTer® Stranded Total RNA-Seq Kit v3 workflow, for example, needs at least 9 operations — adapter removal, UMI extraction, linker masking, poly-A/T trimming — done in the correct order. CutSeq compiles a single library scheme into one native cutadapt pass, so the whole pipeline is one parameter and one command.

Key features

• One-parameter trimming — describe the whole library as a scheme and let CutSeq apply every step automatically.
• Built-in + custom schemes — 70+ bundled libraries (cutseq --list-adapters) or define your own grammar string.
• Barcodes & UMIs — capture and rename inline barcodes / UMIs into read names.
• QC-aware — discard reads with a reason (too_short, too_many_n, …).
• Efficient & reproducible — a single cutadapt pass, no intermediate I/O.

Explore the docs