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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OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.
Nucleic Acids Res. 2013 Apr 9.