Difference between revisions of "GASSST"
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{{Bioinformatics application | {{Bioinformatics application | ||
− | |sw summary=Fast and accurate aligner for short an long reads | + | |sw summary=Fast and accurate aligner for short an long reads |
− | |bio method= | + | |bio method=Sequence alignment, Mapping |
|created by=Guillaume Rizk and Dominique Lavenier | |created by=Guillaume Rizk and Dominique Lavenier | ||
|created at=IRISA-Symbiose | |created at=IRISA-Symbiose | ||
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GASSST is a read mapper with two main objectives: | GASSST is a read mapper with two main objectives: | ||
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- efficient on short 36 bp reads as well as on longer 500bp reads | - efficient on short 36 bp reads as well as on longer 500bp reads | ||
+ | |||
- still efficient with a high error rate and indels. | - still efficient with a high error rate and indels. | ||
Latest revision as of 16:03, 19 December 2015
Application data |
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Created by | Guillaume Rizk and Dominique Lavenier |
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Principal bioinformatics method(s) | Sequence alignment, Mapping |
Created at | IRISA-Symbiose |
Maintained? | Yes |
Input format(s) | FASTA |
Output format(s) | SAM |
Software features | Gapped alignment, short and long reads |
Programming language(s) | C++ |
Licence | CeCILL |
Operating system(s) | Linux |
Summary: Fast and accurate aligner for short an long reads
"Error: no local variable "counter" was set." is not a number.
Description
GASSST is a read mapper with two main objectives:
- efficient on short 36 bp reads as well as on longer 500bp reads
- still efficient with a high error rate and indels.
It uses the traditional "seed and extend" paradigm with a new filtering step to quickly discards most candidate alignment locations.
Links
References
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