.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH FASTQ_MASKER "1" "January 2014" "fastq_masker 0.0.14" "User Commands"
.SH NAME
fastq_masker \- Masks nucleotides with 'N' (or other character) based on quality
.SH 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)
.TP
[\-h]
= This helpful help screen.
.TP
[\-q N]
= Quality threshold \- nucleotides with lower quality will be masked
.IP
Default is 10.
.TP
[\-r C]
= Replace low\-quality nucleotides with character C. Default is 'N'
.TP
[\-z]
= Compress output with GZIP.
.TP
[\-i INFILE]
= FASTQ input file. default is STDIN.
.IP
[\-o OUTFILE] = FASTQ output file. default is STDOUT.
[\-v]         = Verbose \- report number of sequences.
.TP
If [\-o] is specified,
report will be printed to STDOUT.
.IP
If [\-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
.SH SEE ALSO
The quality of this automatically generated manpage might be
insufficient.  It is suggested to visit
.IP
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
.P
to get a better layout as well as an overview about connected
FASTX tools.