Butler enables rapid cloud-based analysis of thousands of human genomes

被引：0

作者：

Sergei Yakneen

Sebastian M. Waszak

Michael Gertz

Jan O. Korbel

机构：

[1] European Molecular Biology Laboratory (EMBL),Institute of Computer Science

[2] Genome Biology Unit,Department of Medical Oncology

[3] Heidelberg University,Department of Biomolecular Engineering

[4] EMBL,UC Santa Cruz Genomics Institute

[5] European Bioinformatics Institute (EMBL-EBI),Biomedical Engineering

[6] Sophia Genetics SA,Institute of Pharmacy and Molecular Biotechnology and BioQuant

[7] Genome Informatics Program,Department of Haematology

[8] Ontario Institute for Cancer Research,Department of Biomedical Data Science

[9] Barcelona Supercomputing Center (BSC),Department of Genetics

[10] Laboratory for Medical Science Mathematics,Department of Biochemistry and Molecular Medicine

[11] RIKEN Center for Integrative Medical Sciences,CIBIO/InBIO—Research Center in Biodiversity and Genetic Resources

[12] RIKEN Center for Integrative Medical Sciences,Department Biochemistry and Molecular Biomedicine

[13] Broad Institute of MIT and Harvard,Department of Pathology

[14] Dana-Farber Cancer Institute,Department of Medicine, Section of Hematology/Oncology

[15] University of California Santa Cruz,Department of Pediatric Immunology, Hematology and Oncology

[16] University of California Santa Cruz,Institute of Medical Science

[17] Oregon Health and Science University,Department of Biochemistry

[18] Division of Theoretical Bioinformatics,Health Sciences Department of Biomedical Informatics

[19] German Cancer Research Center (DKFZ),Department of Health Sciences and Technology

[20] Heidelberg Center for Personalized Oncology (DKFZ-HIPO),Center for Biomolecular Science and Engineering

[21] German Cancer Research Center,Department of Cell and Systems Biology

[22] Heidelberg University,Department of Radiation Oncology

[23] Wellcome Sanger Institute,Institute for Genomics and Systems Biology

[24] Wellcome Genome Campus,Department of Molecular Genetics

[25] University of Cambridge,Computational Biology Program

[26] University of California San Diego,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences

[27] PDXen Biosystems Inc,Finsen Laboratory and Biotech Research & Innovation Centre (BRIC)

[28] Electronics and Telecommunications Research Institute,Department of Urology

[29] Seven Bridges Genomics,Department of Biological Oceanography

[30] Annai Systems,Genome Science Division, Research Center for Advanced Science and Technology

[31] Inc,Department of Surgery

[32] Stanford University School of Medicine,Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, School of Medicine

[33] Stanford University School of Medicine,Department of Oncology, Gil Medical Center

[34] University of Leuven,Department of Bioinformatics and Computational Biology

[35] The Francis Crick Institute,Bioinformatics Core Facility

[36] Computational Biology Program,Heinrich Pette Institute

[37] Ontario Institute for Cancer Research,Ontario Tumour Bank

[38] The Hospital for Sick Children,Department of Pathology

[39] Heidelberg University,Laboratory of Pathology, Center for Cancer Research

[40] New BIH Digital Health Center,Department of Cellular and Molecular Medicine and Department of Bioengineering

[41] Berlin Institute of Health (BIH) and Charité – Universitätsmedizin Berlin,Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre

[42] Rigshospitalet,Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS)

[43] University of Montreal,Department of Zoology, Genetics and Physical Anthropology

[44] Universidade do Porto,The Biomedical Research Centre (CINBIO)

[45] University of Barcelona,Department of Genomic Medicine

[46] Center for Cancer Research,Quantitative and Computational Biosciences Graduate Program

[47] Massachusetts General Hospital,Genome Informatics Program

[48] Massachusetts General Hospital,Institute of Human Genetics

[49] Harvard Medical School,Institute of Human Genetics

[50] University of Chicago,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience

来源：

Nature Biotechnology | 2020年 / 38卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.

引用

页码：288 / 292

页数：4

共 27 条

[1]

Habermann N(2016)Using large-scale genome variation cohorts to decipher the molecular mechanism of cancer C. R. Biol. 339 308-313

[2]

Mardin BR(2017)Nextflow enables reproducible computational workflows Nat. Biotechnol. 35 316-319

[3]

Yakneen S(2017)Toil enables reproducible, open source, big biomedical data analyses Nat. Biotechnol. 35 314-316

[4]

Korbel JO(2017)GenomeVIP: a cloud platform for genomic variant discovery and interpretation Genome Res. 27 1450-1459

[5]

Di Tommaso P(2015)Data analysis: create a cloud commons Nature 523 149-151

[6]

Vivian J(2017)Computing patient data in the cloud: practical and legal considerations for genetics and genomics research in Europe and internationally Genome Med. 9 303-536

[7]

Paten B(2014)Rampant software errors may undermine scientific results F1000 Res. 3 530-1760

[8]

Mashl RJ(2017)A review of bioinformatic pipeline frameworks Brief. Bioinformatics 18 2-i339

[9]

Stein LD(2014)Docker: lightweight Linux containers for consistent development and deployment Linux J. 2014 1754-15.7.12

[10]

Knoppers BM(2009)Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 i333-54

← 1 2 3 →