ssake(1)
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 exten
- sion (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.