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Genome Biol. 2016 Jun 10;17(1):126. doi: 10.1186/s13059-016-0993-1.

Resolving complex structural genomic rearrangements using a randomized approach.

Author information

1
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
2
Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
3
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. remills@umich.edu.
4
Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA. remills@umich.edu.

Abstract

Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome or represent different overlapping events on homologous chromosomes. We present SVelter, an algorithm that identifies regions of the genome suspected to harbor a complex event and then resolves the structure by iteratively rearranging the local genome structure, in a randomized fashion, with each structure scored against characteristics of the observed sequencing data. SVelter is able to accurately reconstruct complex chromosomal rearrangements when compared to well-characterized genomes that have been deeply sequenced with both short and long reads.

KEYWORDS:

Complex structural rearrangements; Copy number variant (CNV); Human; Sequence analysis; Structural variation (SV)

PMID:
27287201
PMCID:
PMC4901421
DOI:
10.1186/s13059-016-0993-1
[Indexed for MEDLINE]
Free PMC Article
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