Accelerating minimap2 for whole-genome alignment.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41712760.
- Also identified by DOI 10.1093/bioinformatics/btag083 and PMC identifier 12980334.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Recent advances in long-read sequencing and genome assembly techniques have enabled the generation of high-quality assemblies, often comprising megabase-scale sequences that span entire chromosomes. This results in longer but fewer sequences per genome, which affects the parallelization efficiency of whole-genome alignment tools. Current methods that assign one thread per query sequence now face suboptimal CPU use and longer runtimes because the processing of fewer sequences leaves many threads idle. We present mm2-plus, a fast and efficient method for whole-genome alignment, built upon the commonly used minimap2 aligner. Our improvements include a fine-grained parallel chaining algorithm and a fast method for differentiating primary and secondary chains. These optimizations accelerate the alignment of human, plant, and primate genomes by 1.6× to 7.2× without compromising accuracy. Source code is available at https://github.com/at-cg/mm2-plus and https://doi.org/10.5281/zenodo.18220923.
Medical subject headings
- Software
- Sequence Alignment
- Genome
- Genomics
- Whole Genome Sequencing