ReplaceTagWithLetter #

Replace sequence bases in tagged regions with a specified letter.

[[step]]
    action = "ReplaceTagWithLetter"
    label = "mytag"  # Tag containing regions to replace
    letter = "N"   # Replacement character (defaults to 'N')

This transformation replaces all sequence bases within the regions defined by a tag with a specified replacement character. Quality scores are preserved unchanged. This is commonly used to mask low-quality regions as ‘N’ characters.

Parameters #

• label: Name of the tag containing regions to be replaced
• letter: Single character to replace bases with (defaults to ‘N’ if not specified)

Example Use Cases #

• Mask low-quality bases identified by ExtractRegionsOfLowQuality
• Replace specific sequence motifs identified by other extraction steps
• Convert tagged regions to ambiguous bases for downstream analysis

The tag must have been created by a previous extraction step and must contain location information.