ssake - assembling millions of very short DNA sequences
Progressive assembly of millions of short DNA sequences by k-mer
search through a prefix tree and 3' extension.
- -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)
/usr/share/doc/ssake/SSAKE.readme between
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.