NAME
ssake - assembling millions of very short DNA sequences
SYNOPSIS
Progressive assembly of millions of short DNA sequences by k-mer search
through a prefix tree and 3’ extension.
OPTIONS
-f Fasta file containing all the [paired (-p 1) / unpaired (-p 0)]
reads (required) paired reads must now be separated by ":"
-s Fasta file containing sequences to use as seeds exclusively
(specify only if different from read set, optional)
-m Minimum number of overlapping bases with the seed/contig during
overhang consensus build up (default -m 16)
-o Minimum number of reads needed to call a base during an
extension (default -o 3)
-r Minimum base ratio used to accept a overhang consensus base
(default -r 0.7)
-t Trim up to -t base(s) on the contig end when all possibilities
have been exhausted for an extension (default -t 0)>
-p Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)
-v Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)
-b Base name for your output files (optional)
============ Options below only considered with -p 1 ============
-d Mean distance expected/observed between paired-end reads
(default -d 200, optional)
-e Error (%) allowed on mean distance e.g. -e 0.75 == distance
+/- 75% (default -e 0.75, optional)
-k Minimum number of links (read pairs) to compute scaffold
(default -k 2, optional)
-a Maximum link ratio between two best contig pairs *higher values
lead to least accurate scaffolding* (default -a 0.70, optional)
-z Minimum contig size to track paired-end reads (default -z 50,
optional)
-g Fasta file containing unpaired sequence reads (optional)
SEE ALSO
/usr/share/doc/ssake/SSAKE.readmee between
AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for
the Debian 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.
On Debian systems, the complete text of the GNU General Public License
can be found in /usr/share/common-licenses/GPL.
January 2008