AStarix: Fast and Optimal Sequence-to-Graph Alignment

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 AS tarix . Experimental evaluation of AS tarix 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 .