RT Journal Article
SR Electronic
T1 Meta-aligner: Long-read alignment based on genome statistics
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 060129
DO 10.1101/060129
A1 Damoun Nashta-ali
A1 Ali Aliyari
A1 Mohammad Amin Edrisi
A1 Ahmad Ahmadian Moghadam
A1 Seyed Abolfazl Motahari
A1 Babak Hossein Khalaj
YR 2016
UL http://biorxiv.org/content/early/2016/06/21/060129.abstract
AB Fast and accurate alignment of long-reads plays an important role in reducing the overall cost of long-read sequencing. In this paper, we propose Meta-aligner, an efficient and accurate long-read aligner that exploits the statistics of reference genome to improve performance in terms of reducing time complexity and achieving significantly higher recall for very noisy and long reads. The first step of algorithm adopts well-known short-read aligners in order to rapidly align a large fraction of reads through a progressive process of aligning read fragments to the reference genome. In the second phase, the remaining reads are handled by simultaneous alignment of all read fragments and a decision making process which exploits the overall information provided by the corresponding mapped fragments. By using this procedure, significant performance improvement is attained in comparison with traditional schemes in the case of PacBio long-reads.