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.\"     Title: sspace
.\"    Author: [see the "AUTHORS" section]
.\" Generator: Asciidoctor 1.5.4
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "SSPACE" "1" "" "\ \&" "\ \&"
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.SH "NAME"
sspace \- SSPACE\-basic scaffolding tool
.SH "SYNOPSIS"
.sp
\fBsspace\fP [options] \-l [libraryfilename]  \-s [contigfilename]
.SH "DESCRIPTION"
.sp
SSPACE is a script able to extend and scaffold pre\-assembled contigs using one or more mate pairs or paired\-end libraries, or even a combination.
.sp
Please read the README file at /usr/share/doc/sspace/README.gz for more information.
.SH "OPTIONS"
.SS "General Parameters"
.sp
\fB\-l\fP
.RS 4
Library file containing two paired read files with insert size, error and either mate pair or paired end indication (REQUIRED)
.RE
.sp
\fB\-s\fP
.RS 4
FASTA file containing contig sequences used for extension. Inserted pairs are mapped to extended and non\-extended contigs (REQUIRED)
.RE
.sp
\fB\-x\fP
.RS 4
Indicate whether to extend the contigs of \-s using paired reads in \-l (\-x 1=extension, \-x 0=no extension, default \-x 0)
.RE
.SS "Extension Parameters"
.sp
\fB\-m\fP
.RS 4
Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default \-m 32)
.RE
.sp
\fB\-o\fP
.RS 4
Minimum number of reads needed to call a base during an extension (default \-o 20)
.RE
.sp
\fB\-t\fP
.RS 4
Trim up to \-t base(s) on the contig end when all possibilities have been exhausted for an extension (default \-t 0)
.RE
.sp
\fB\-u\fP
.RS 4
FASTA/FASTQ file containing unpaired sequence reads (optional)
.RE
.sp
\fB\-r\fP
.RS 4
Minimum base ratio used to accept a overhang consensus base (default \-r 0.9)
.RE
.SS "Scaffolding Parameters"
.sp
\fB\-z\fP
.RS 4
Minimum contig length used for scaffolding. Filters out contigs below this value (default \-z 0)
.RE
.sp
\fB\-k\fP
.RS 4
Minimum number of links (read pairs) to compute scaffold (default \-k 5)
.RE
.sp
\fB\-a\fP
.RS 4
Maximum link ratio between two best contig pairs. \fBHigher values lead to least accurate scaffolding\fP (default \-a 0.7)
.RE
.sp
\fB\-n\fP
.RS 4
Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default \-n 15)
.RE
.SS "Bowtie Parameters"
.sp
\fB\-g\fP
.RS 4
Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the \-v option in Bowtie. Higher number of allowed gaps can lead to least accurate scaffolding. (default \-g 0)
.RE
.sp
\fB\-T\fP
.RS 4
Specify the number of threads in Bowtie. Corresponds to the \-p/\-\-threads option in Bowtie (default \-T 1)
.RE
.SS "Additional Parameters"
.sp
\fB\-b\fP
.RS 4
Base name for your output files (default \-b standard_output)
.RE
.sp
\fB\-v\fP
.RS 4
Runs in verbose mode (\-v 1=yes, \-v 0=no, default \-v 0)
.RE
.sp
\fB\-p\fP
.RS 4
Make .dot file for visualisation (\-p 1=yes, \-p 0=no, default \-p 0)
.RE
.SH "AUTHORS"
.sp
Marten Boetzer, Walter Pirovano, Nicola Soranzo