by quality score fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}' #if $mask_type.value == 'lowercase' --lowercase #else -m '${mask_type}' #end if N's Lowercase Less than or equal Less than Equal to Not Equal to Greater than Greater than or equal

**What it does** This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method. This tool is not available for use on color space (csSanger) formats.