Quick Start

Installation

pip install cutseq

Basic Usage

Trim adapters using a built-in scheme:

cutseq -A TAKARAV3 test_R1.fq.gz test_R2.fq.gz

Or specify a custom adapter scheme:

cutseq -a "ACACGACGCTCTTCCGATCTXXX<XXXXXXNNNNNNNNAGATCGGAAGAGCACACGTC" test_R1.fq.gz test_R2.fq.gz

The scheme string describes the structure of your library:

• Outermost: Illumina adapters
• Inner: Inline barcodes or custom primers (in parentheses)
• Next: UMI sequences (N)
• Next: Masked sequences (X)
• Center: Library insert (>, <, or - for orientation)

See the documentation for more details.