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.