Making the difference: integrating structural variation detection tools

From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have recently been developed, spurred by the advent of th...

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Bibliographic Details
Published in:Briefings in bioinformatics 2015-09, Vol.16 (5), p.852-864
Main Authors: Lin, Ke, Smit, Sandra, Bonnema, Guusje, Sanchez-Perez, Gabino, de Ridder, Dick
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatica
Bioinformatics
Biological variation
BIOS Applied Bioinformatics
Biotechnology
Communities
Data Interpretation, Statistical
EPS
Genetics, Population
Genome
Genomes
Genomics
Genotype & phenotype
High-Throughput Nucleotide Sequencing
Laboratorium voor Plantenveredeling
Laboratory of Plant Breeding
Mapping
Phenotypic variations
Pipelines
Plant Breeding
PRI BIOS Applied Bioinformatics
Speciation
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Summary:From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have recently been developed, spurred by the advent of the next-generation sequencing technology. Such callers mainly exploit split-read mapping or paired-end read mapping. However, as different callers are geared towards different types of structural variation, there is still no single caller that can be considered a community standard; instead, increasingly the various callers are combined in integrated pipelines. In this article, we review a wide range of callers, discuss challenges in the integration step and present a survey of pipelines used in population genomics studies. Based on our findings, we provide general recommendations on how to set-up such pipelines. Finally, we present an outlook on future challenges in structural variation detection.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbu047