abPOA：一个基于 SIMD 的 C 库，用于使用自适应带实现快速偏序比对。
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band.
机构信息
Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
出版信息
Bioinformatics. 2021 Aug 9;37(15):2209-2211. doi: 10.1093/bioinformatics/btaa963.
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 10 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.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
部分排序比对（将序列与有向无环图比对）现在经常被用作长读测序错误纠正和组装的关键组成部分。我们提出了 abPOA（自适应带状部分排序比对），这是一个基于单指令多数据（SIMD）的 C 库，用于使用自适应带状动态规划进行快速部分排序比对。它可以作为独立的多序列比对和共识调用工具，也可以轻松集成到任何长读测序错误纠正和组装工作流程中。与最先进的工具（SPOA）相比，abPOA 的速度快 10 倍，且具有相当的比对准确性。
可用性和实现
abPOA 是用 C 语言实现的。一个独立的工具和一个 C/Python 软件接口可在 https://github.com/yangao07/abPOA 上免费获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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