KegAlign: Optimizing pairwise alignments with diagonal partitioning.

ABSTRACT: Our ability to generate sequencing data and assemble it into high quality complete genomes has rapidly advanced in recent years. These data promise to advance our understanding of organismal biology and answer longstanding evolutionary questions. Multiple genome alignment is a key tool in this quest. It is also the area which is lagging: today we can generate genomes faster than we can construct and update multiple alignments containing them. The bottleneck is in considerable computational time required to generate accurate pairwise alignments between divergent genomes, an unavoidable precursor to multiple alignments. This step is typically performed with lastZ, a very sensitive and yet equally slow tool. Here we describe an optimized GPU-enabled pairwise aligner KegAlign. It incorporates

SUBMITTER: Gulhan AB 

PROVIDER: S-EPMC11398343 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature