Provided by: fastx-toolkit_0.0.14-1_amd64
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 (firstname.lastname@example.org) [-h] = 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' [-z] = 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.
The quality of this automatically generated manpage might be insufficient. It is suggested to visit http://hannonlab.cshl.edu/fastx_toolkit/commandline.html to get a better layout as well as an overview about connected FASTX tools.