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 protected]
= 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.