NAME

       fastq_masker - Masks nucleotides with 'N' (or other character) based on quality

DESCRIPTION

       usage: fastq_masker [-h] [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.14 by
       A. Gordon (assafgordon@gmail.com)

       [-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.

       [-Q N] = FASTQ ASCII offset. Default is 33.

SEE ALSO

       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.

fastq_masker 0.0.14                                August 2017                                   FASTQ_MASKER(1)