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Updated: Dec 1, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Yan Gao1,2, Yongzhuang Liu1, Yanmei Ma1
1Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
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.
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