2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2014
Abstrakt

Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schonhuth. CLEVER: clique-enumerating variant finder. Bioinformatics, 28(22):2875-2882. 2012.

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Abstract:

MOTIVATION: Next-generation sequencing techniques have facilitated a large-scale 
analysis of human genetic variation. Despite the advances in sequencing speed,
the computational discovery of structural variants is not yet standard. It is
likely that many variants have remained undiscovered in most sequenced
individuals. RESULTS: Here, we present a novel internal segment size based
approach, which organizes all, including concordant, reads into a read alignment 
graph, where max-cliques represent maximal contradiction-free groups of
alignments. A novel algorithm then enumerates all max-cliques and statistically
evaluates them for their potential to reflect insertions or deletions. For the
first time in the literature, we compare a large range of state-of-the-art
approaches using simulated Illumina reads from a fully annotated genome and
present relevant performance statistics. We achieve superior performance, in
particular, for deletions or insertions (indels) of length 20-100 nt. This has
been previously identified as a remaining major challenge in structural variation
discovery, in particular, for insert size based approaches. In this size range,
we even outperform split-read aligners. We achieve competitive results also on
biological data, where our method is the only one to make a substantial amount of
correct predictions, which, additionally, are disjoint from those by split-read
aligners. AVAILABILITY: CLEVER is open source (GPL) and available from
http://clever-sv.googlecode.com. CONTACT: as@cwi.nl or tm@cwi.nl. SUPPLEMENTARY
INFORMATION: Supplementary data are available at Bioinformatics online.