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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Veröffentlicht in:PLOS ONE Jg. 10; H. 8; S. e0135800
Hauptverfasser: Bao, Riyue, Hernandez, Kyle, Huang, Lei, Kang, Wenjun, Bartom, Elizabeth, Onel, Kenan, Volchenboum, Samuel, Andrade, Jorge
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Public Library of Science (PLoS) 13.08.2015
Public Library of Science
Schlagworte:
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
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Zusammenfassung: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.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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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