.TH KMER-MASK "1" "May 2015" "kmer-mask 0~20150520+2004" "User Commands"
.SH NAME
kmer-mask \- mask and filter set of nucleotide sequences by kmer content
.SH SYNOPSIS
.B kmer\-mask
.RB { \-novel | \-confirmed }
.RB [ \-mdb
.IR mer-database ]
.RB [ \-ms
.IR mer-size ]
.RB [ \-edb
.IR exist-database ]
.RB [ \-m
.IR min-size ]
.RB [ \-e
.IR extend-size]
.RB [ \-lowthreshold
.IR l ]
.RB [ \-highthreshold
.IR h ]
.RB [ \-t
.IR threads ]
.RB [ \-v ]
.RB [ \-h
.IR histogram ]
.RB [ \-promote | \-demote | \-discard ]
.BI \-1 \0in.1.fastq
.RB [ \-2
.IR in.2.fastq ]
.BI \-o \0output-prefix
.SH DESCRIPTION
Mask and filter set of sequences (presumed to be reads) by kmer content.
Masking can be done to retain novel sequence not in the database, or to retain
confirmed sequence present in the database.
Filtering will segregate sequences fully, partially or not masked.
.SH OPTIONS
.TP
.BI \-mdb \0mer\-database
load masking kmers from
.BR meryl (1)
.I mer\-database
.TP
.BI \-ms \0mer\-size
.TP
.BI \-edb \0exist\-database
save masking kmers to an
.BR existDB (1)
file
.I exist\-database
for faster restarts
.TP
.BI \-1 \0in.1.fastq
.TP
.BI \-2 \0in.2.fastq
input reads files in fastq, fastq.gz, fastq.bz2 or fastq.xz format.
The second is optional, but messes up the output classification if not present.
.TP
.BI \-o \0out
.RS
prefix for output reads
.TP
\fIout\fR.fullymasked.[12].fastq
reads with below 'lowthreshold' bases retained
.TP
.IR out .partiallymasked.[12].fastq
reads in between
.TP
.IR out .retained.[12].fastq
reads with more than 'hightreshold' bases retained
.TP
.IR out .discarded.[12].fastq
reads with conflicting status
.RE
.TP
.BI \-m \0min\-size
ignore database hits below this many consecutive kmers (0)
.TP
.BI \-e \0extend\-size
extend database hits across this many missing kmers (0)
.TP
.B \-novel
RETAIN novel sequence not present in the database
.TP
.B \-confirmed
RETAIN confirmed sequence present in the database
.TP
.B \-promote
promote the lesser RETAINED read to the status of the more RETAINED read
read1=fullymasked and read2=partiallymasked \-> both are partiallymasked
.TP
.B \-demote
demote the more RETAINED read to the status of the lesser RETAINED read
read1=fullymasked and read2=partiallymasked \-> both are fullymasked
.TP
.B \-discard
discard pairs with conflicting status (DEFAULT)
read1=fullymasked and read2=partiallymasked \-> both are discarded
.SS "stats on stderr, number of sequences with amount RETAINED:"
.TP
.BI \-lowthreshold \0t
(0.3333)
.TP
.BI \-highthreshold \0t
(0.6667)
.TP
.BI \-h \0histogram
write a histogram of the amount of sequence RETAINED
.TP
.BI \-t \0t
use
.I t
compute threads
.TP
\fB\-v\fR
show progress
.SH SEE ALSO
.BR meryl (1)
.BR existDB (1)