Fig. 2: LexicMap alignment workflow.
From: Efficient sequence alignment against millions of prokaryotic genomes with LexicMap
a, The same LexicHash hash functions (one per probe) used in the indexing step are used here, applied to the query to capture one prefix-matching k-mer per probe. b, For each probe, the seed data are scanned to find prefix or suffix matches ≥ 15 bp. The common prefix or suffix constitutes an anchor. c, The variable-length anchors are chained using a modified version of the Minimap2 algorithm. d,e, Fast pseudoalignment (d) is followed by base-level alignment (e) using the wavefront alignment algorithm. Note that, in b, only prefix matching is illustrated, whereas suffix matching is not shown for simplicity.
