Prowler: a novel trimming algorithm for Oxford Nanopore sequence data

Trimming and filtering tools are useful in DNA sequencing analysis because they increase the accuracy of sequence alignments and thus the reliability of results. Oxford nanopore technologies (ONT) trimming and filtering tools are currently rudimentary, generally only filtering reads based on whole read average quality. This results in discarding reads that contain regions of high-quality sequence. Here, we propose Prowler, a trimmer that uses a window-based approach inspired by algorithms used to trim short read data. Importantly, we retain the phase and read length information by optionally replacing trimmed sections with Ns.