Difference between revisions of "AGILE"
(Created page with "{{Bioinformatics application |sw summary=A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, cust...") |
|||
| Line 2: | Line 2: | ||
|sw summary=A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process | |sw summary=A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process | ||
|bio method=Mapping | |bio method=Mapping | ||
| + | |bio tech=454, | ||
| + | |created at=Northwestern University | ||
| + | |input format=FASTA, | ||
| + | |output format=PSL, AXT, MAF, SIM4, BLAST | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| + | AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200. In comparison with existing tools, the most significant features of AGILE are: | ||
| + | * High flexibility. It allows a large number of mismatches and insertions/deletions in mapping. Current version of AGILE has been tested to work with upto 10% differences in mapping. | ||
| + | |||
| + | * High Sensitivity. AGILE correctly maps about ~99.8% reads. | ||
| + | |||
| + | * Ability to handle large datasets. We have successfully tested AGILE with human genome and a million batch queries. | ||
| + | |||
| + | * Speed. Using AGILE, we can map approximately 1.1 million reads of length 500 each to a reference human genome per hour. That means about 550 million bases per hour. At this rate, AGILE will need only 6 hours for a 1X coverage of the human genome. | ||
Revision as of 10:22, 7 September 2011
|
Application data |
|
| Principal bioinformatics method(s) | Mapping |
|---|---|
| Technology | 454 |
| Created at | Northwestern University |
| Maintained? | Maybe |
| Input format(s) | FASTA |
| Output format(s) | PSL, AXT, MAF, SIM4, BLAST |
Summary: A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process
"Error: no local variable "counter" was set." is not a number.
Description
AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200. In comparison with existing tools, the most significant features of AGILE are:
- High flexibility. It allows a large number of mismatches and insertions/deletions in mapping. Current version of AGILE has been tested to work with upto 10% differences in mapping.
- High Sensitivity. AGILE correctly maps about ~99.8% reads.
- Ability to handle large datasets. We have successfully tested AGILE with human genome and a million batch queries.
- Speed. Using AGILE, we can map approximately 1.1 million reads of length 500 each to a reference human genome per hour. That means about 550 million bases per hour. At this rate, AGILE will need only 6 hours for a 1X coverage of the human genome.
Links
References
To add a reference for AGILE, enter the PubMed ID in the field below and click 'Add'.
Search for "AGILE" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
