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.\"     Title: kmc_tools-filter
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "KMC_TOOLS\-FILTER" "1" "" "\ \&" "\ \&"
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.SH "NAME"
kmc_tools-filter \- filter out reads with too small number of k\-mers
.SH "SYNOPSIS"
.sp
\fBkmc_tools filter\fP <kmc_input_db> [kmc_input_db_params] <input_read_set> [input_read_set_params] <output_read_set> [output_read_set_params]
.SH "DESCRIPTION"
.sp
This command filters out reads with too small number of k\-mers.
.SH "OPTIONS"
.sp
.if n .RS 4
.nf
.fam C
For k\-mers database there are additional parameters:
.fam
.fi
.if n .RE
.sp
\fB\-ci<value>\fP
.RS 4
exclude k\-mers occurring less than <value> times
.RE
.sp
\fB\-cx<value>\fP
.RS 4
exclude k\-mers occurring more of than <value> times
.RE
.sp
For the input set of reads there are additional parameters:
.sp
\fB\-ci<value>\fP
.RS 4
remove reads containing less k\-mers than value. It can be integer or floating number in range [0.0;1.0]
.RE
.sp
\fB\-ci<value>\fP
.RS 4
remove reads containing more k\-mers than value. It can be integer or floating number in range [0.0;1.0]
.RE
.sp
\fB\-f<a/q>\fP
.RS 4
input in FASTA format (\-fa), FASTQ format (\-fq); default: FASTQ
.sp
.if n .RS 4
.nf
.fam C
For the output set of reads there are additional parameters:
.fam
.fi
.if n .RE
.RE
.sp
\fB\-f<a/q>\fP
.RS 4
output in FASTA format (\-fa), FASTQ format (\-fq); default: same as input
.RE
.SH "EXAMPLE"
.sp
.if n .RS 4
.nf
.fam C
kmc_tools filter kmc_db \-ci3 input.fastq \-ci0.5 \-cx1.0 filtered.fastq
kmc_tools filter kmc_db input.fastq \-ci10 \-cx100 filtered.fastq
.fam
.fi
.if n .RE
.SH "AUTHOR"
.sp
KMC was originally written by:
.sp
.RS 4
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Sebastian Deorowicz (\c
.MTO "sebastian.deorowicz\(atpolsl.pl" "" ")"
.RE
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.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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Marek Kokot
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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.el \{\
.  sp -1
.  IP \(bu 2.3
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Szymon Grabowski
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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.el \{\
.  sp -1
.  IP \(bu 2.3
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Agnieszka Debudaj\-Grabysz
.RE
.SH "COPYING"
.sp
KMC is a free software distributed under GNU GPL3 licence for academic,
research, and commercial use.