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 …
MJ Bauer, AJ Cox, G Rosone - Theoretical Computer Science, 2013 - Elsevier
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 …
M Vyverman, B De Baets, V Fack… - Nucleic acids …, 2012 - academic.oup.com
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 …
TH Dadi, E Siragusa, VC Piro, A Andrusch… - …, 2018 - academic.oup.com
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) …