High-speed and accurate color-space short-read alignment with CUSHAW2

High-speed and accurate color-space short-read alignment with CUSHAW2
Yongchao Liu, Bernt Popp, Bertil Schmidt
(Submitted on 17 Apr 2013)

Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real color-space mate-paired reads to the human genome. The results show that CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and BFAST at an order-of-magnitude faster speed and significantly smaller peak resident memory size. Availability: CUSHAW2 and all simulated datasets are available at this http URL Contact: liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de

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