Strategies for assembling large, complex genomes have evolved to include a combination of
whole-genome shotgun sequencing and hierarchal map-assisted sequencing 1 , 2 . Whole-…

… They regard the collection as a single concatenated text T[1 . .n] with separator symbols, …
However, they are unable to locate where those positions are in T unless they add a set of …

… Since the eighth 1 in B L is B L [ 10 ] and it is preceded by two 0s, we see that ACG’s outgoing
edges’ labels are in EBWT [ 8..10 ] ⁠, so they are A, C and T. Suppose we want to follow …

… that σ is the effective alphabet of T, that is, the σ symbols appear in T. This implies that σ ≤
r … data structure the position i in T of the first character of the phrase containing T[k], take the …

Recently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store
thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to …

… We first show that T∩ has at most α leaves of T. The leaves of T∩ that are also leaves of T
correspond to the symbols that belong to the intersection, and thus to the number of 0s in any …

The famous Burrows–Wheeler Transform (BWT) was originally defined for a single string but
variations have been developed for sets of strings, labeled trees, de Bruijn graphs, etc. In …

The mammalian tongue is believed to fall into a class of organs known as muscular hydrostats,
organs for which muscle contraction both generates and provides the skeletal support for …

… lexicographical suffix of T. The BWT … T, as well as for locating all offsets in T where a substring
occurs. Only O(r) space is needed overall. More details can be found in the study of Gagie …

To store and search genomic databases efficiently, researchers have recently started building
compressed self-indexes based on straight-line programs and LZ77. In this paper we …