RT Journal Article
SR Electronic
T1 abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.07.083196
DO 10.1101/2020.05.07.083196
A1 Gao, Yan
A1 Liu, Yongzhuang
A1 Ma, Yanmei
A1 Liu, Bo
A1 Wang, Yadong
A1 Xing, Yi
YR 2020
UL http://biorxiv.org/content/early/2020/05/10/2020.05.07.083196.abstract
AB Summary Partial order alignment, which aligns a sequence to a directed acyclic graph, is now frequently used as a key component in long-read error correction and assembly. We present abPOA (adaptive banded Partial Order Alignment), a Single Instruction Multiple Data (SIMD) based C library for fast partial order alignment using adaptive banded dynamic programming. It can work as a stand-alone multiple sequence alignment and consensus calling tool or be easily integrated into any long-read error correction and assembly workflow. Compared to a state-of-the-art tool (SPOA), abPOA is up to 15 times faster with a comparable alignment accuracy.Availability and implementation abPOA is implemented in C. A stand-alone tool and a C/Python software interface are freely available at https://github.com/yangao07/abPOA.Contact ydwang{at}hit.edu.cn or XINGYI{at}email.chop.eduCompeting Interest StatementY.X. is a scientific cofounder of Panorama Medicine.