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.