Jekyll2022-11-30T05:14:56+00:00https://zhanghaowen.com/feed.xmlHaowen ZhangHaowen ZhangGraph Wavefront Algorithm2022-07-04T00:00:00+00:002022-07-04T00:00:00+00:00https://zhanghaowen.com/Graph-wavefront-algorithm<h1 id="graph-wavefront-algorithm">Graph wavefront algorithm</h1>
<p>Recently, we have proposed graph wavefront algorithm, which is an efficient sequence-to-graph alignment algorithm in practice. The implementation termed Gwfa is available <a href="https://github.com/lh3/gwfa">here</a>. Tested on 4 real sequence graphs, Gwfa with a pruning heuristic achieved up to 5 orders of magnitude speedup compared with other sequence-to-graph alignment methods.</p>
<p>Though the Gwfa <a href="https://arxiv.org/abs/2206.13574">preprint</a> contains a formal description of the algorithm, it might not be easy for one without any experience in wavefront alignment algorithm (WFA) to understand. Therefore, I made a <a href="https://youtu.be/ycS2oNUpt0g">tutorial video</a> to explain the idea on how Gwfa works with an example. The slides are available <a href="/assets/Gwfa%20tutorial.pdf">here</a>. Hope these materials can be helpful.</p>Haowen ZhangGraph wavefront algorithm