ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification

Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publ...

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Vydáno v:	PLOS ONE Ročník 10; číslo 8; s. e0135800
Hlavní autoři:	Bao, Riyue, Hernandez, Kyle, Huang, Lei, Kang, Wenjun, Bartom, Elizabeth, Onel, Kenan, Volchenboum, Samuel, Andrade, Jorge
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science (PLoS) 13.08.2015 Public Library of Science
Témata:	Algorithms Alignment Archives & records Bioinformatics Cancer Cancer genetics Cloud computing Computation Computational Biology Computer programs Computers Consortia Data analysis Data processing Exome Exome - genetics Freeware Gene sequencing Genetic aspects Genetic diversity Genetic variance Genomes Genomics Germ-Line Mutation Germ-Line Mutation - genetics High performance computing Humans Informatics Interactive control Internet Medicine Mutation Mutation - genetics Pediatrics Pipelining (computers) Q Quality control R Reproducibility Reproducibility of Results Research Article Researchers Science Sensitivity analysis Software Source code United States > US Illinois Chicago Illinois
ISSN:	1932-6203, 1932-6203
On-line přístup:	Získat plný text
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Shrnutí:	Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publicly-available software for the detection of germline and somatic variants, concordance is generally limited among variant callers and alignment algorithms. Successful integration of variants detected by multiple methods requires in-depth knowledge of the software, access to high-performance computing resources, and advanced programming techniques. We present ExScalibur, a set of fully automated, highly scalable and modulated pipelines for whole exome data analysis. The suite integrates multiple alignment and variant calling algorithms for the accurate detection of germline and somatic mutations with close to 99% sensitivity and specificity. ExScalibur implements streamlined execution of analytical modules, real-time monitoring of pipeline progress, robust handling of errors and intuitive documentation that allows for increased reproducibility and sharing of results and workflows. It runs on local computers, high-performance computing clusters and cloud environments. In addition, we provide a data analysis report utility to facilitate visualization of the results that offers interactive exploration of quality control files, read alignment and variant calls, assisting downstream customization of potential disease-causing mutations. ExScalibur is open-source and is also available as a public image on Amazon cloud.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: RB KH LH SV JA. Performed the experiments: RB KH LH WK. Analyzed the data: RB KH LH. Contributed reagents/materials/analysis tools: KO EB. Wrote the paper: RB KH LH WK EB KO SV JA. Developed and implemented the pipelines and software: RB KH. Evaluated the pipelines: RB KH LH. Built Amazon EC2 environments: WK. Competing Interests: The authors have declared that no competing interests exist. Current address: Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois, United States of America
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0135800