ExtractRegionsOfLowQuality #

Extract regions where bases have quality scores below threshold, with a minimum length requirement.

[[step]]
    action = "ExtractRegionsOfLowQuality"
    segment = "read1" # Any of your input segments
    min_quality = 60  # Quality threshold (Phred+33)
    min_length = 5    # Minimum region length (bp)
    out_label = "low_quality_regions"

This transformation scans through quality scores of the specified segment and identifies contiguous regions where quality scores are below the specified threshold. Each low-quality region that meets the minimum length requirement becomes a tagged region with location information (start position and length).

Parameters #

• segment: Which read to analyze for low-quality regions
• min_quality: Quality score threshold using Phred+33 encoding. See Phred quality score for ASCII character mapping
• min_length: Minimum length (in bases) for a region to be extracted. Must be >= 1
• out_label: Tag name to store the extracted regions

Example #

With min_quality = 60 (ASCII ‘<’) and min_length = 5, any contiguous stretches of 5+ bases with quality scores below ‘<’ will be identified as low-quality regions. This is useful for masking or filtering poor-quality sequences.

Notes #

Note that one read may have multiple low-quality regions. TrimAtTag will cut at the outmost one of them.