fastq_masker - Masks nucleotides with 'N' (or other character) based on quality
usage: fastq_masker [-h] [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE] Part
of FASTX Toolkit 0.0.14 by A. Gordon (email@example.com)
- = This helpful help screen.
- [-q N]
- = Quality threshold - nucleotides with lower quality will be masked
- Default is 10.
- [-r C]
- = Replace low-quality nucleotides with character C. Default is 'N'
- = Compress output with GZIP.
- [-i INFILE]
- = FASTQ input file. default is STDIN.
- [-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose -
report number of sequences.
- If [-o] is specified,
- report will be printed to STDOUT.
- If [-o] is not specified (and output goes to STDOUT), report will be
printed to STDERR.
- [-Q N]
- = FASTQ ASCII offset. Default is 33.