Two decades ago, a breakthrough in indexing string collections made it possible to
represent them within their compressed space while at the same time offering indexed …

The analysis of biological sequencing data has been one of the biggest applications of
string algorithms. The approaches used in many such applications are based on the …

Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of 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 …

Abstract The Burrows-Wheeler Transform (BWT) is an invertible text transformation that
permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the …

Motivation Plasmids and other mobile elements are central contributors to microbial
evolution and genome innovation. Recently, they have been found to have important roles in …

Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

Abstract 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 …

We address the problem of designing, implementing, and experimenting with compressed
data structures that support rank and select queries over a dictionary of integers. We shine a …

The suffix array SA [1.. n] of a text T of length n is a permutation of {1,…, n} describing the
lexicographical ordering of suffixes of T and is considered to be one of the most important …