Title: Meander : visually exploring the structural variome using space-filling curves
Authors: Pavlopoulos GA, Georgios ×
Kumar, Parveen
Sifrim, Alejandro
Sakai, Ryo
Lin, Meng Lay
Voet, Thierry
Moreau, Yves
Aerts, Jan #
Issue Date: Jun-2013
Publisher: Oxford University Press
Series Title: Nucleic acids research vol:41 issue:11 pages:e118
Article number: e118
Abstract: The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and and can be run on any platform. It can be found at∼bioiuser/meander.
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Department of Human Genetics - miscellaneous
Laboratory of Reproductive Genomics
ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
× corresponding author
# (joint) last author

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