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bioRxiv · 10.1101/2020.01.22.915496

AStarix: Fast and Optimal Sequence-to-Graph Alignment

Ivanov, P.·Bichsel, B.·Mustafa, H.·Kahles, A.·Rätsch, G.·Vechev, M.
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Abstract

We present an algorithm for the optimal alignment of sequences to genome graphs. It works by phrasing the edit distance minimization task as finding a shortest path on an implicit alignment graph. To find a shortest path, we instantiate the A[*] paradigm with a novel domain-specific heuristic function that accounts for the upcoming subsequence in the query to be aligned, resulting in a provably optimal alignment algorithm called ASO_SCPLOWTARIXC_SCPLOW. Experimental evaluation of ASO_SCPLOWTARIXC_SCPLOW shows that it is 1-2 orders of magnitude faster than state-of-the-art optimal algorithms on the task of aligning Illumina reads to reference genome graphs. Implementations and evaluations are available at https://github.com/eth-sri/astarix.

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Ivanov, P., Bichsel, B., Mustafa, H., Kahles, A., Rätsch, G., Vechev, M.. 2020-01-23. AStarix: Fast and Optimal Sequence-to-Graph Alignment. https://doi.org/10.1101/2020.01.22.915496

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