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.readme between
AUTHORS
This manual page was written by Andreas Tille <tille [AT] 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.