xenial (1) fastq_masker.1.gz

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.

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.