'\" t
.\"     Title: gt-readjoiner-prefilter
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-READJOINER\-PREF" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-readjoiner-prefilter \- Remove contained and low\-quality reads and encode read set in GtEncseq format\&.
.SH "SYNOPSIS"
.sp
\fBgt readjoiner prefilter\fR [option \&...]
.SH "DESCRIPTION"
.PP
\fB\-readset\fR [\fIstring\fR]
.RS 4
specify the readset name default: filename of first input sequence_file
.RE
.PP
\fB\-db\fR
.RS 4
specify a list of input libraries (Fasta/FastQ); for single\-end libraries use the filename (which is not allowed to contain
\fI:\fR
symbols); for paired\-end libraries with reads interleaved (f,r,f,r,\&...) in a single file use the notation <filename>:<insertlength>[,<stdev>] (stdev may be omitted); for paired\-end with reads in two files (f, r) use the notation <file_f>:<file_r>:<insertlength>[,<stdev>]
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-q\fR [\fIyes|no\fR]
.RS 4
suppress standard output messages (default: no)
.RE
.PP
\fB\-des\fR [\fIyes|no\fR]
.RS 4
store Fasta IDs (or entire descriptionsif used together with \-clipdes no) warning: increases the memory requirement (default: no)
.RE
.PP
\fB\-clipdes\fR [\fIyes|no\fR]
.RS 4
clip Fasta descriptions after first space set to false if you need entire descriptions (default: yes)
.RE
.PP
\fB\-memdes\fR [\fIyes|no\fR]
.RS 4
use memory storage for descriptions (default: use temporary disk storage)
.RE
.PP
\fB\-maxlow\fR [\fIvalue\fR]
.RS 4
maximal number of low\-quality positions in a read default: infinite
.RE
.PP
\fB\-lowqual\fR [\fIvalue\fR]
.RS 4
maximal quality for a position to be considered low\-quality (default: 3)
.RE
.PP
\fB\-phred64\fR [\fIyes|no\fR]
.RS 4
use phred64 scores for FastQ format (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help for basic options and exit
.RE
.PP
\fB\-help+\fR
.RS 4
display help for all options and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.