Compute resources available to the research community for microbiome analysis

dc.altmetrics.display
dc.contributor.authorPapudeshi, Bhavya
dc.contributor.authorSanders, Sheri
dc.contributor.authorGanote, Carrie
dc.contributor.authorDoak, Tom
dc.date.accessioned2019-01-16T19:38:13Z
dc.date.available2019-01-16T19:38:13Z
dc.date.issued2019-01-16
dc.description.abstractThe National Center for Genome Analysis Support (NCGAS) is an NSF-funded center tasked with assisting biologists in getting access to computational resources they need in order to analyze genomic data. To support microbiome analysis, NCGAS provides preconfigured virtual machines (VM) to identify taxa in 16S amplicon sequencing, and to identify both taxa and functions from whole genome metagenomes. Additionally, a pipeline to reconstruct genomes from metagenomes, to examine the role of specific microbes in a community, is available as a preconfigured VM hosting Anvi’o (https://ncgas.org/Blog_Posts/Running%20Anvio%20on%20Jetstream.php). Jetstream, a cloud computing resource, is both easy to use and flattens the learning curve for using the Linux operating system and for installing bioinformatics software. Jetstream provides an environment for both prototyping and publishing tailored workflows. Through an NCGAS allocation, a researcher can get access to Jetstream, and to other national compute clusters with more memory and for parallel processing. These compute resources have Globus connect subscriptions which assists in transferring terabytes of data quickly. In this workshop, we will demonstrate how to get an NCGAS allocation, set up a Jetstream account, spin up a preconfigured virtual machine for microbiome analysis (https://ncgas.org/Blog_Posts/Getting%20Started%20on%20Jetstream.php), and transfer data between compute clusters using Globus (https://ncgas.org/Blog_Posts/Getting%20Started%20with%20Globus.php).en
dc.description.sponsorshipThis research is based upon work supported by the National Science Foundation under grant No. ABI-1759906 to Indiana University.en
dc.identifier.citationPapudeshi, B., S. Sanders, C. Ganote, T. Doak. 2019. Compute resources available to the research community for microbiome analysis. Plant and Animal Genomes XXVII, San Diego, CA. Retrieved from http://hdl.handle.net/2022/22655.en
dc.identifier.urihttps://hdl.handle.net/2022/22655
dc.language.isoenen
dc.publisherPlant and Animal Genome XXVIIen
dc.rightsExcept where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This license includes the following terms: You are free to share -to copy, distribute and transmit the work and to remix -to adapt the work under the following conditions: attribution -you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectNCGASen
dc.subjectMicrobiomeen
dc.subjectJetstreamen
dc.subjectVirtual Machinesen
dc.titleCompute resources available to the research community for microbiome analysisen
dc.typePresentationen

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