SSAKE is a genomics application for assembling millions of very short DNA sequences.
The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
*Best performance is achieved by quality-trimming your reads before assembly
Enjoy SSAKE responsibly!
SSAKE is written in PERL and runs on Linux. SSAKE cycles through short sequence reads stored in a hash table and progressively searches through a prefix tree for the longest possible identical overlap between any two sequences. The algorithm was used to assemble 25-36 bp sequence reads from viral, bacterial and fungal genomes and on forty millions 25-mers simulated using the whole-genome shotgun (WGS) sequence data from the Sargasso sea metagenomics project. Considering the number of sequences to assemble, SSAKE is robust and tractable.
René L Warren, Granger G Sutton, Steven JM Jones, Robert A Holt. 2007 (epub 2006 Dec 8). Assembling millions of short DNA sequences using SSAKE. bioinformatics. 23:500-501.
Copyright (c) 2006-2011 Canada's Michael Smith Genome Science Centre. All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
René Warren, Granger Sutton, Steven Jones and Robert Holt
Released Dec 24, 2013
fixed SSAKE for Perl >= 5.16.0, where deprecated getopts.pl has been removed. Thanks to Nicola Soranzo for sending the fix.
More about this release…
- Get SSAKE for all platforms
- If you are using Plone 3.2 or higher, you probably want to install this product with buildout. See our tutorial on installing add-on products with buildout for more information.
|3.8.1||Dec 24, 2013||fixed SSAKE for Perl >= 5.16.0, where deprecated getopts.pl has been removed. Thanks to Nicola Soranzo for sending the fix. More about this release…||AFL||final|
|3.8||May 03, 2011||v3.8+ is 30% faster than the previous release. Additional assembly control has been implemented (-w) that limits the generation of low depth of coverage contigs More about this release…||GPL||final|
|3.7||Nov 17, 2010||version 3.7 has improved support for seed-based assemblies, notably read-space restriction to that of the seed sequence (TASR behavior) More about this release…||GPL||final|
|3.6||Aug 25, 2010||v3.6 accepts an infinite number of sequence size libraries and offers preliminary support for paired-end Sanger reads. More about this release…||GPL||final|
|3.5||May 28, 2010||v3.5+ Uses mate pairs to help resolve repeats (preventing contig misassemblies) at run time and attempts to force-fill gaps with redundant sequences (improves contiguity and repeat resolution). More about this release…||GPL||final|
|3.4||Apr 14, 2009||Version 3.4 exploits paired-end reads to explore possible contig merges within scaffolds and allows users to track read position and individual base coverage for reads *fully embedded* within contigs. More about this release…||GPL||final|
|3.2.1||Mar 31, 2009||Optimized prefix tree implementation for faster assemblies with decreased memory usage. More about this release…||AFL||final|
|3.2||Dec 07, 2007||SSAKE 3.2 adjusts contig ends to find new extension possibilities. A bug that prevented SSAKE from exploring the entire read space for contig extensions seeded by shorter reads has been FIXED More about this release…||GPL||final|
|2.0||SSAKE can now handle error-rich [short sequence] data sets. For each seed sequence or contig being extended, SSAKE looks through the entire overlapping k-mer space and generates a consensus sequence from overhanging bases - It then extends contigs using that consensus, provided the bases it comprises pass user-defined thresholds. More about this release…||GPL||beta|