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bioRxiv · 10.1101/2024.11.25.625328

Accelerating whole-genome alignment in the age of complete genome assemblies

Chandra, G.·Vasimuddin, M.·Misra, S.·Jain, C.
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Abstract

Recent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spanning entire chromosomes. The increase in the assembly contiguity and the reduced number of assembly contigs also implies that whole-genome alignment is no longer an embarrassingly parallel problem. The conventional method of aligning sequences of the query genome in parallel is to utilize a single thread per sequence. This results in poor CPU utilization and long runtimes. In this work, we designed optimizations to accelerate whole-genome alignment on multi-core processors and implemented them in a commonly used aligner, minimap2. Our improvements include a fine-grained parallel chaining method and a fast mechanism for differentiating primary and secondary chains. Our approach accelerates alignment of human, plant, and primate genomes by 1.6x to 7.2x without compromising accuracy.

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Chandra, G., Vasimuddin, M., Misra, S., Jain, C.. 2024-11-28. Accelerating whole-genome alignment in the age of complete genome assemblies. https://doi.org/10.1101/2024.11.25.625328

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