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Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study

  • Gaurav Kaushik
  • Brandi Davis-DusenberyEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1878)

Abstract

The Seven Bridges Cancer Genomics Cloud (CGC) is part of the National Cancer Institute Cloud Resource project, which was created to explore the paradigm of co-locating massive datasets with the computational resources to analyze them. The CGC was designed to allow researchers to easily find the data they need and analyze it with robust applications in a scalable and reproducible fashion. To enable this, individual tools are packaged within Docker containers and described by the Common Workflow Language (CWL), an emerging standard for enabling reproducible data analysis. On the CGC, researchers can deploy individual tools and customize massive workflows by chaining together tools. Here, we discuss a case study in which RNA sequencing data is analyzed with different methods and compared on the Seven Bridges CGC. We highlight best practices for designing command line tools, Docker containers, and CWL descriptions to enable massively parallelized and reproducible biomedical computation with cloud resources.

Key words

Cloud Bioinformatics Cancer informatics TCGA AWS Docker Reproducibility Software design 

Notes

Acknowledgements

The Cancer Genomics Cloud is powered by Seven Bridges and has been funded in whole or in part with federal funds from the NCI, NIH, Department of Health and Human Services, under contract no. HHSN261201400008C and HHSN261200800001E. We thank the entire Seven Bridges team, the Cancer Genomics Cloud Pilot teams from the NCI, the Broad Institute, and the Institute of Systems Biology, the Genomic Data Commons team, countless early users, and data donors. We also wish to further acknowledge the source of two of the datasets that are available to authorized users through the CGC and that were central to its development: The Cancer Genome Atlas (TCGA, phs000178). The resources described here were developed in part based upon data generated by The Cancer Genome Atlas managed by the NCI and NHGRI. Information about TCGA can be found at https://cancergenome.nih.gov/. And Therapeutically Applicable Research to Generate Effective Treatments (TARGET, phs000218). The resources described here were developed in part based on data generated by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative managed by the NCI.

References

  1. 1.
    Alioto TS et al (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun 6:10001CrossRefGoogle Scholar
  2. 2.
    Lau JW, Lehnert E, Sethi A, Malhotra R, Kaushik G, Onder Z, Groves-Kirkby N (2017) The cancer genomics cloud: Collaborative, reproducible, and democratized-a new paradigm in large-scale computational research. Cancer Research. 77(21):e3–e6CrossRefGoogle Scholar
  3. 3.
    Merkel D (2014) Docker: lightweight linux containers for consistent development and deployment. Linux J 2014(239):2Google Scholar
  4. 4.
    Amstutz, Peter, Crusoe, Michael R, Tijanić, Nebojša, Chapman, Brad, Chilton, John, Heuer, Michael, Kartashov, Andrey, Leehr, Dan, Ménager, Hervé, Nedeljkovich, Maya, Scales, Matt, Soiland-Reyes, Stian, Stojanovic, Luka (2016) Common workflow language, v1.0. FigshareGoogle Scholar
  5. 5.
    Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12(1):1CrossRefGoogle Scholar
  6. 6.
    Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34(5):525–527CrossRefGoogle Scholar
  7. 7.
    Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ et al (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483(7391):603–607CrossRefGoogle Scholar
  8. 8.
    Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T et al (2002) The Ensembl genome database project. Nucleic Acids Res 30(1):38–41CrossRefGoogle Scholar
  9. 9.
    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Foundation MedicineCambridgeUSA
  2. 2.Seven Bridges GenomicsCambridgeUSA

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