OLego, A Sensitive Splice Mapper

OLego, A Sensitive Splice Mapper

  • April 8, 2013

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a multiple-seed-and-extend 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 the Burrows-Wheeler transform (BWT) and FM-index. This approach also makes it particularly sensitive for discovering small exons. OLego is implemented in C++ with full support for multithreading, enabling fast processing of large-scale data.

  • Jie Wu, Olga Anczuków, Adrian R. Krainer, Michael Q. Zhang, Chaolin Zhang. OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research, 2013, 41(10):5149-5163. Link
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