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. 2016 Oct 27;4:e2619. doi: 10.7717/peerj.2619

Figure 3. Suffix trie paths for the BWA and PARA-suite.

Figure 3

Paths of the algorithms through the suffix trie aligning the read sequence GCCATG$ against the reference sequence GTTATG$ (where $ means the end of a sequence). The red dotted line represents the algorithm of the BWA aligner, allowing for two mismatches; the blue dashed line indicates the BWA PARA algorithm. The underlined bases represent positions where the respective aligner introduces a mismatch. The example shows that BWA PARA needs 14 comparisons but the basic BWA needs 16 comparisons. Indels are not shown for simplicity.