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bioRxiv · 10.1101/2020.05.07.083196

abPOA: an SIMD-based C library for fast partialorder alignment using adaptive band

GAO, Y.·Liu, Y.·Ma, Y.·Liu, B.·Wang, Y.·Xing, Y.
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Abstract

SummaryPartial 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 implementationabPOA is implemented in C. A stand-alone tool and a C/Python software interface are freely available at https://github.com/yangao07/abPOA. Contactydwang@hit.edu.cn or XINGYI@email.chop.edu

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GAO, Y., Liu, Y., Ma, Y., Liu, B., Wang, Y., Xing, Y.. 2020-05-10. abPOA: an SIMD-based C library for fast partialorder alignment using adaptive band. https://doi.org/10.1101/2020.05.07.083196

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