abPOA: an SIMD-based C library for fast partial order alignment using adaptive band.

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Partial order alignment is vital for long-read sequencing data processing.
• Existing tools can be computationally intensive, limiting scalability.

Purpose of the Study:

• To develop a faster and efficient partial order alignment tool.
• To improve long-read error correction and assembly workflows.

Main Methods:

• Implemented adaptive banded dynamic programming using Single Instruction Multiple Data (SIMD).
• Developed abPOA as a C library with a stand-alone tool and C/Python interface.

Main Results:

• abPOA achieves up to 10x speed improvement over SPOA.
• Maintained comparable alignment accuracy to state-of-the-art methods.
• Demonstrated utility as a stand-alone tool and for integration into existing pipelines.

Conclusions:

• abPOA offers a significant performance enhancement for partial order alignment.
• The tool facilitates more efficient long-read error correction and genome assembly.
• abPOA is readily available for research and development.