Sequence alignment is a long standing problem in bioinformatics. The Basic Local
Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools …

De novo genome sequence assembly is important both to generate new sequence
assemblies for previously uncharacterized genomes and to identify the genome sequence of …

Abstract Motivation: Eugene Myers in his string graph paper suggested that in a string graph
or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also …

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 …

A repetitive sequence collection is a set of sequences which are small variations of each
other. A prominent example are genome sequences of individuals of the same or close …

Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although
each path in the graph is a potential haplotype, most paths are non-biological, unlikely …

Recent progress in the field of DNA sequencing motivates us to consider the problem of
computing the Burrows–Wheeler transform (BWT) of a collection of strings. A human …

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 …

The combination of incessant advances in sequencing technology producing large amounts
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …

Motivation Mapping-based approaches have become limited in their application to very
large sets of references since computing an FM-index for very large databases (eg> 10 GB) …