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

Kathrin Trappe, Anne-Katrin Emde, Hans-Christian Ehrlich, Knut Reinert. Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics, 2014.

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Abstract:

MOTIVATION: The landscape of structural variation (SV) including complex
duplication and translocation patterns is far from resolved. SV detection tools
usually exhibit low agreement, are often geared toward certain types or size
ranges of variation and struggle to correctly classify the type and exact size of
SVs. RESULTS: We present Gustaf (Generic mUlti-SpliT Alignment Finder), a sound
generic multi-split SV detection tool that detects and classifies deletions,
inversions, dispersed duplications and translocations of >/=30 bp. Our approach
is based on a generic multi-split alignment strategy that can identify SV
breakpoints with base pair resolution. We show that Gustaf correctly identifies
SVs, especially in the range from 30 to 100 bp, which we call the next-generation
sequencing (NGS) twilight zone of SVs, as well as larger SVs >500 bp. Gustaf
performs better than similar tools in our benchmark and is furthermore able to
correctly identify size and location of dispersed duplications and
translocations, which otherwise might be wrongly classified, for example, as
large deletions. Availability and implementation: Project information, paper
benchmark and source code are available via http://www.seqan.de/projects/gustaf/.
CONTACT: kathrin.trappe@fu-berlin.de.