OLego
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Application data |
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| Created by | Wu Jie, Zhang Chaolin |
|---|---|
| Biological application domain(s) | Genomics, RNA-Seq, RNA-Seq alignment |
| Principal bioinformatics method(s) | Read mapping, Sequence alignment |
| Technology | Illumina |
| Created at | Cold Spring Harbor Laboratory, Rockefeller University |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | SAM, BED |
| Software features | capable of using very small seeds for splice Read mapping, but still fast and accurate |
| Programming language(s) | C++ |
| Licence | GPLv3 |
| Operating system(s) | Linux, Linux 64, Mac OS X |
Summary: OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.
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