Read Trimming

DRAGEN can remove artifacts from reads using hardware accelerated read trimming. Hardware accelerated read trimming is available on U200 and AWS systems, as part of the DRAGEN mapper and adds no additional run time. To enable the trimmer in normal mode, use --read-trimmers. To enable the trimmer in soft mode, use --soft-read-trimmers.

In normal trimming mode, potential artifacts are removed from input reads. Reads which are trimmed to fewer than 20 bases are filtered and replaced with a dummy read consisting of 10 N bases. In addition, the filtered reads have 0x200 SAM flag set.

DRAGEN contains a novel lossless soft-trimming mode. In soft-trimming mode, reads are mapped as though they had been trimmed, but no bases are removed. The intention of soft trimming is to suppress systematic mismapping of reads containing trimmable artifacts, such as Poly-G artifacts, from getting mapped to reference G homopolymers or adapter sequences getting mapped to matching reference loci, without actually losing the trimmed bases in aligned output. Soft trimming for Poly-G artifacts is enabled by default on supported systems.