skewer

Skewer is a bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and is specifically designed for processing NGS pair-end sequences. For input, it accepts the adapter sequence to be trimmed and the forward/reverse reads.

For additional information and examples please see Skewer documentation.

ml biocontainers skewer
skewer -x <adapter sequence> -q 3 <forward reads.gz> <reverse reads.gz>

Parallel Capabilities: Single core default, multithreading options supported.