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.

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Total input reads—Total number of reads in the input files.

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Total input bases—Total number of bases in the input reads.

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Total input bases R1—Total number of bases in R1 reads.

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Total input bases R2—Total number of bases in R2 reads.

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Average input read length—Total number of input bases divided by the number of input reads.

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Total trimmed reads—Total number of reads trimmed by at least one base, not including soft-trimming.

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Total trimmed bases—Total number of bases trimmed, not including soft-trimming.

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Average bases trimmed per read—The number of trimmed bases divided by the number of input reads.

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Average bases trimmed per trimmed read—The number of trimmed bases divided by the number of trimmed reads.

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Remaining poly-G K-mers R1 3prime—The number of R1 3' read ends that contain likely Poly-G artifacts after trimming.

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Remaining poly-G K-mers R2 3prime—The number of R2 3' read ends thatcontain likely Poly-G artifacts after trimming.

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Poly-G trimmed reads—The number of reads with at least one base trimmed during Poly-G artifact trimming. This metric is reported for both mates (R1 and R2) and the filtering status (unfiltered and filtered) of the trimmed read. The metric includes reads which were trimmed during soft-trimming.

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Poly-G trimmed bases—The number of bases trimmed during Poly-G artifact trimming. This metric is reported for both mates (R1 and R2) and the filtering status (unfiltered and filtered) of the trimmed read. The metric includes bases from reads which were trimmed during soft-trimming.

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Total filtered reads—The number of reads that were filtered out during trimming.

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Reads filtered for minimum read length R1—The number of R1 reads that were filtered due to being trimmed below the minimum read length.

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Reads filtered for minimum read length R2—The number of R2 reads that were filtered due to being trimmed below the minimum read length.