Data sets in large applications are often too massive to fit completely inside the computers
internal memory. The resulting input/output communication (or I/O) between fast internal …

The devices forming Internet of Things (IoT) networks need to be re-programmed over the
air, so that new features are added, software bugs or security vulnerabilities are resolved …

Suffix trees and suffix arrays are widely used and largely interchangeable index structures
on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space …

Motivation: Sequence assembly is a difficult problem whose importance has grown again
recently as the cost of sequencing has dramatically dropped. Most new sequence assembly …

Data sets in large applications are often too massive to fit completely inside the computer's
internal memory. The resulting input/output communication (or I/O) between fast internal …

We present the software library Stxxl that is an implementation of the C++ standard template
library (STL) for processing huge data sets that can fit only on hard disks. It supports parallel …

The longest-common-prefix (LCP) array is an adjunct to the suffix array that allows many
string processing problems to be solved in optimal time and space. Its construction is a …

We present Masai, a read mapper representing the state-of-the-art in terms of speed and
accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times …

This article presents an O (n)-time algorithm called SACA-K for sorting the suffixes of an
input string T [0, n-1] over an alphabet A [0, K-1]. The problem of sorting the suffixes of T is …

In this paper we describe algorithms for computing the Burrows-Wheeler Transform (bwt)
and for building (compressed) indexes in external memory. The innovative feature of our …