.TH "SSAKE" "1" "January 2008"
.SH "NAME"
ssake \- assembling millions of very short DNA sequences

.SH SYNOPSIS
Progressive assembly of millions of short DNA sequences by k-mer search
through a prefix tree and 3' extension.

.SH "OPTIONS"
.PP
.IP \-f
Fasta file containing all the [paired (\-p 1) / unpaired (\-p 0)] reads (required) \fBpaired reads must now be separated by ":"\fR
.IP \-s
Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)
.IP \-m
Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default \-m 16)
.IP \-o
Minimum number of reads needed to call a base during an extension (default \-o 3)
.IP \-r
Minimum base ratio used to accept a overhang consensus base (default \-r 0.7)
.IP \-t
Trim up to \-t base(s) on the contig end when all possibilities have been exhausted for an extension (default \-t 0)>
.IP -p
Paired-end reads used? (\-p 1=yes, \-p 0=no, default \-p 0)
.IP \-v
Runs in verbose mode (\-v 1=yes, \-v 0=no, default \-v 0, optional)
.IP \-b
Base name for your output files (optional)
.PP
============ Options below only considered with \-p 1 ============
.IP \-d
Mean distance expected/observed between paired-end reads (default \-d 200, optional)
.IP -e
Error (%) allowed on mean distance   e.g. \-e 0.75  == distance +/- 75% (default \-e 0.75, optional)
.IP \-k
Minimum number of links (read pairs) to compute scaffold (default \-k 2, optional)
.IP \-a
Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default \-a 0.70, optional)
.IP \-z
Minimum contig size to track paired-end reads (default \-z 50, optional)
.IP \-g
Fasta file containing unpaired sequence reads (optional)

.SH SEE ALSO
/usr/share/doc/ssake/SSAKE.readme between

.SH "AUTHORS"
.PP
This manual page was written by Andreas Tille <tille@debian.org> for
the \fBDebian\fP system (but may be used by others).  Permission is
granted to copy, distribute and/or modify this document under
the terms of the GNU General Public License, Version 2 any
later version published by the Free Software Foundation.

.PP
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.