Difference between revisions of "SSAKE"
m (Text replace - "bio method=Assembly" to "bio method=Sequence assembly") |
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ACGATAGCTTCG:ACGCGATAGATC | ACGATAGCTTCG:ACGCGATAGATC | ||
| − | |bio method= | + | |bio method=Sequence assembly, |
|input format=FASTA, special format for paired reads | |input format=FASTA, special format for paired reads | ||
|output format=FASTA | |output format=FASTA | ||
Latest revision as of 04:49, 25 August 2015
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Application data |
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| Principal bioinformatics method(s) | Sequence assembly |
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| Maintained? | Maybe |
| Input format(s) | FASTA, special format for paired reads |
| Output format(s) | FASTA |
| Programming language(s) | Perl |
| Licence | GPLv2 |
| Operating system(s) | Linux |
Summary: 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. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux. Please note that paired reads need to be in one pseuod fasta line separated by ':'
>readpair:1000 ACGATAGCTTCG:ACGCGATAGATC
"Error: no local variable "counter" was set." is not a number.
Links
References
To add a reference for SSAKE, enter the PubMed ID in the field below and click 'Add'.
Search for "SSAKE" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
