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.