Fastbreak: a Tool for Analysis and Visualization of Structural Variations in Genomic Data

Overview

Journal EURASIP J Bioinform Syst Biol

Publisher Springer

Specialty Biology

Date 2012 Oct 11

PMID 23046488

Citations 2

Authors

Ryan Bressler

Jake Lin

Andrea Eakin

Thomas Robinson

Richard Kreisberg

Hector Rovira

Theo Knijnenburg

John Boyle

Ilya Shmulevich

Affiliations

Soon will be listed here.

Abstract

Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas.

Citing Articles

Visualization tools for human structural variations identified by whole-genome sequencing.

Yokoyama T, Kasahara M J Hum Genet. 2019; 65(1):49-60.

PMID: 31666648 PMC: 8075883. DOI: 10.1038/s10038-019-0687-0.

ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation.

Sante T, Vergult S, Volders P, Kloosterman W, Trooskens G, De Preter K PLoS One. 2014; 9(12):e113800.

PMID: 25503062 PMC: 4264741. DOI: 10.1371/journal.pone.0113800.

References

Clark M, Homer N, OConnor B, Chen Z, Eskin A, Lee H . U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet. 2010; 6(1):e1000832. PMC: 2813426. DOI: 10.1371/journal.pgen.1000832. View

Chen K, Wallis J, McLellan M, Larson D, Kalicki J, Pohl C . BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009; 6(9):677-81. PMC: 3661775. DOI: 10.1038/nmeth.1363. View

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

. Integrated genomic analyses of ovarian carcinoma. Nature. 2011; 474(7353):609-15. PMC: 3163504. DOI: 10.1038/nature10166. View

Feuk L, Carson A, Scherer S . Structural variation in the human genome. Nat Rev Genet. 2006; 7(2):85-97. DOI: 10.1038/nrg1767. View