KegAlign: Optimizing pairwise alignments with diagonal partitioning

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 a new parallelization strategy, diagonal partitioning, with the latest features of modern GPUs. With KegAlign a typical human/mouse alignment can be computed in under 6 hours on a machine containing a single NVidia A100 GPU and 80 CPU cores without the need for any pre-partitioning of input sequences: a ∼150× improvement over lastZ. While other pairwise aligners can complete this task in a fraction of that time, none achieves the sensitivity of KegAlign’s main alignment engine, lastZ, and thus may not be suitable for comparing divergent genomes. In addition to providing the source code and a Conda package for KegAlign we also provide a Galaxy workflow that can be readily used by anyone.