AGILE
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Application data |
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| Created by | Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok Choudhary |
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| Principal bioinformatics method(s) | Mapping |
| Technology | 454 |
| Created at | Electrical Engineering & Computer Science, Northwestern University |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | PSL, AXT, MAF, SIM4, BLAST |
| Programming language(s) | C |
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
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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.
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References
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