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. Author manuscript; available in PMC: 2020 Nov 2.
Published in final edited form as: Nat Biotechnol. 2019 Aug 2;37(8):907–915. doi: 10.1038/s41587-019-0201-4

Figure 2.

Figure 2.

Overview of HISAT2’s indexes and alignment output

(a) Hierarchical indexing in the hierarchical graph FM index (HGFM). Hierarchical indexing consists of two types of indexes: (1) a global index that represents the entire human genome and (2) 55,172 overlapping local indexes that collectively cover the genome plus all variants. When both are graph FM indexes, a genome plus a large collection of variants can be searched simultaneously. (b) A repeat index represents genomic sequences that are identical. (c) A read matching repeat sequences (e.g., Read3 and Read4) is aligned to just one location (the repeat sequence). (d) The corresponding genomic locations of repeat aligned reads are retrieved via APIs.