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. DRAGEN provides multiple independent trimming filters that target different types of artifacts or use cases. You can enable and configure the artifacts or use cases independently to tailor the read-trimming to your analysis. Read trimming uses two different modes, hard-trimming and soft-trimminh.

To enable hard-trimming mode, use --read-trimmers. In hard-trimming mode, potential artifacts are removed from input reads. Reads that are trimmed to fewer than 20 bases are filtered and replaced with a placeholder read that uses 10 N bases. DRAGEN assigns the filtered reads a 0x200 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. To enable the trimmer in soft mode, use --soft-read-trimmers.

Soft-trimming suppresses systematic mismapping of reads that contain trimmable artifacts, without actually losing the trimmed bases in aligned output. Soft-trimming prevents reads with trimmable artifacts, such as Poly-G artifacts, from being mapped to reference G homopolymers, or prevents adapter sequences from being mapped to the matching reference loci. Soft-trimming might map reads to different positions in the reference than they would have been if not using soft-trimming. When using soft-trimmed, DRAGEN does not filter reads and does not map reads with bases that would have been trimmed entirely.

Soft-trimming for Poly-G artifacts is enabled by default on supported systems.

Read Trimming Metrics

The trimmer generates a metrics file titled <output prefix>.trimmer_metrics.csv. Metrics are available on an aggregate level over all input data. The metrics units are in reads or bases.

Metric	Description
Total input reads	Total number of reads in the input files.
Total input bases	Total number of bases in the input reads.
Total input bases R1	Total number of bases in R1 reads.
Total input bases R2	Total number of bases in R2 reads.
Average input read length	Total number of input bases divided by the number of input reads.
Total trimmed reads	Total number of reads trimmed by at least one base, not including soft-trimming.
Total trimmed bases	Total number of bases trimmed, not including soft-trimming.
Average bases trimmed per read	The number of trimmed bases divided by the number of input reads.
Average bases trimmed per trimmed read	The number of trimmed bases divided by the number of trimmed reads.
Remaining poly-G K-mers R1 3prime	The number of R1 3' read ends that contain likely Poly-G artifacts after trimming.
Remaining poly-G K-mers R2 3prime	The number of R2 3' read ends that contain likely Poly-G artifacts after trimming.
Total filtered reads	The number of reads that were filtered out during trimming.
Reads filtered for minimum read length R1	The number of R1 reads that were filtered out due to being trimmed below the minimum read length.
Reads filtered for minimum read length R2	The number of R2 reads that were filtered out due to being trimmed below the minimum read length.
<Trimmer tool> trimmed reads	The number of reads with at least one base trimmed by TRIMMER. DRAGEN reports the metric for both R1 and R2 mates and the filtering status (unfiltered or filtered) of the trimmed read. The metric includes reads that were trimmed during soft-trimming. Each trimming tool above produces the metric.
<Trimmer tool> trimmed bases	The number of bases trimmed by TRIMMER. The metric is produced for both R1 and R2 mates and the filtering status (unfiltered or filtered) of the trimmed read. The metric includes bases from reads that were trimmed during soft trimming. Each trimming tool above produces the metric.

Read Trimming Settings

Use the following options to configure read trimming.

Metric	Description
--read-trimmers	To enable trimming filters in hard-trimming mode, set to a comma-separated list of the trimmer tools you would like to use. To disable trimming, set to none. During mapping, artifacts are removed from all reads. Read trimming is disabled by default. The following are valid trimmer names: fixed-len—Fixed-length trimming polyg—Poly-G trimming quality—Quality trimming adapter—Adapter trimming n—Ambiguous base trimming min-len—Minimum length trimming cut-end—Maximum length trimming
--soft-read-trimmers	To enable trimming filters in soft-trimming mode, set to a comma-separated list of the trimmer tools you would like to use. To disable soft trimming, set to none. During mapping, reads are aligned as if trimmed, and bases are not removed from the reads. The following are the valid trimmer names. Soft-trimming is enabled for the polyg filter by default. fixed-len—Fixed-length trimming polyg—Poly-G trimming quality—Quality trimming adapter—Adapter trimming n—Ambiguous base trimming min-len—Minimum length trimming cut-end—Maximum length trimming
--trimming-only	Disables mapping and alignment to run read-trimming only.
--trim-min-length	Specify a minimum read length. DRAGEN filters any reads with a length less than the value after read-trimming is completed.
--trim-min-quality	Specify the minimum read quality. DRAGEN trims bases from the 3' end of reads with a quality below the value.
--trim-adapter-read1	Specify the file that contains adapter sequences to trim from the 3' end of Read 1.
--trim-adapter-read2	Specify the file that contains adapter sequences to trim from the 3' end of Read 2.
--trim-adapter-stringency	Specify the minimum number of adapter bases required for trimming.
--trim-max-length	Specify the maximum number of bases that can be trimmed from the sequences of both reads.