KegAlign: optimizing pairwise alignments with diagonal partitioning

Ahmed Burak Gulhan

doi:10.1186/s13059-025-03830-0

2025-11-18

DOI：10.1186/s13059-025-03830-0

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摘要

En 中文

测序和组装技术的进步使得创建数千个基因组组装成为可能。然而，由于成对比对过程耗时，生成其分析所需的多个比对滞后，该过程通常由速度慢但敏感的工具lastZ执行。在此，我们开发了KegAlign，一种优化的GPU加速成对比对工具。KegAlign采用一种新颖的对角线分区并行化策略，并利用先进的GPU功能。它可以在不进行预分区的情况下，在配备GPU的节点上用不到6小时完成人类/小鼠比对，同时保持对分歧基因组至关重要的lastZ级敏感度。KegAlign可作为源代码、Conda软件包以及用户友好的Galaxy工作流提供。

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期刊

Genome Biology

IF:

9.4

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6.4K

被引数:

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university of california santa cruz

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penn state university

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