fastq_masker(1) 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.
= 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.