External memory BWT and LCP computation for sequence collections with applications
Background Sequencing technologies produce larger and larger collections of
biosequences that have to be stored in compressed indices supporting fast search …
biosequences that have to be stored in compressed indices supporting fast search …
FSG: fast string graph construction for de novo assembly
The string graph for a collection of next-generation reads is a lossless data representation
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
T Beller, E Ohlebusch - Algorithms for Molecular Biology, 2016 - Springer
Abstract Background Recently, Marcus et al.(Bioinformatics 30: 3476–83, 2014) proposed to
use a compressed de Bruijn graph to describe the relationship between the genomes of …
use a compressed de Bruijn graph to describe the relationship between the genomes of …
LSG: an external-memory tool to compute string graphs for next-generation sequencing data assembly
The large amount of short read data that has to be assembled in future applications, such as
in metagenomics or cancer genomics, strongly motivates the investigation of disk-based …
in metagenomics or cancer genomics, strongly motivates the investigation of disk-based …
An external-memory algorithm for string graph construction
Some recent results (Bauer et al. in Algorithms in bioinformatics, Springer, Berlin, pp 326–
337, 2012; Cox et al. in Algorithms in bioinformatics, Springer, Berlin, pp. 214–224, 2012; …
337, 2012; Cox et al. in Algorithms in bioinformatics, Springer, Berlin, pp. 214–224, 2012; …
Simulating the DNA overlap graph in succinct space
D Díaz-Domínguez, T Gagie… - 30th Annual Symposium …, 2019 - drops.dagstuhl.de
Converting a set of sequencing reads into a lossless compact data structure that encodes all
the relevant biological information is a major challenge. The classical approaches are to …
the relevant biological information is a major challenge. The classical approaches are to …
Simulating the dna string graph in succinct space
Converting a set of sequencing reads into a lossless compact data structure that encodes all
the relevant biological information is a major challenge. The classical approaches are to …
the relevant biological information is a major challenge. The classical approaches are to …
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings
P Bonizzoni, G Della Vedova, S Nicosia… - arXiv preprint arXiv …, 2016 - arxiv.org
Indexing of very large collections of strings such as those produced by the widespread
sequencing technologies, heavily relies on multi-string generalizations of the Burrows …
sequencing technologies, heavily relies on multi-string generalizations of the Burrows …
FSG: fast string graph construction for de novo assembly of reads data
The string graph for a collection of next-generation reads is a lossless data representation
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
Self-indexing for de novo assembly
M Previtali - 2017 - boa.unimib.it
For at least three decades computer science approaches have proved to be of utmost
importance for extrapolating knowledge from biological data. Indeed, the amount of data …
importance for extrapolating knowledge from biological data. Indeed, the amount of data …