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 …

Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

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 …

Genomics analyses use large reference sequence collections, like pangenomes or
taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both …

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 …

Lempel–Ziv (LZ77) compression is the most commonly used lossless compression
algorithm. The basic idea is to greedily break the input string into blocks (called “phrases”) …

We consider the problem of computing the Maximal Exact Matches (MEMs) of a given
pattern $ P [1.. m] $ on a large repetitive text collection $ T [1.. n] $, which is represented as a …

The sensitivity of a string compression algorithm C asks how much the output size C (T) for
an input string T can increase when a single character edit operation is performed on T. This …

Indexing highly repetitive strings (ie, strings with many repetitions) for fast queries has
become a central research topic in string processing, because it has a wide variety of …

In recent years, the focus of bioinformatics research has moved from individual sequences to
collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform …