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fastq_masker - Masks nucleotides with 'N' (or other character) based on quality

FASTQ_MASKER(1) User Commands FASTQ_MASKER(1)

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.
August 2017 fastq_masker 0.0.14