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Instrumenting Genomic Sequence Analysis Pipeline Mothur on Shared Memory Architecture

Published: 13 July 2014 Publication History

Abstract

Mothur is an open source bioinformatics pipeline used for biological sequence analysis that has gained increasing attention in the microbial ecology community. Because a large set of functionalities in Mothur are memory bound, it is well suited for shared memory architectures, such as the Nautilus supercomputer. In this paper, we present performance results for several commands in Mothur that are popular in the operational taxonomic unit analysis, and show that Nautilus can accelerate pipeline processes many orders of magnitude faster.

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Cited By

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  • (2020)Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing DataFrontiers in Genetics10.3389/fgene.2020.60309311Online publication date: 30-Nov-2020

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  1. Instrumenting Genomic Sequence Analysis Pipeline Mothur on Shared Memory Architecture

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    Published In

    cover image ACM Other conferences
    XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment
    July 2014
    445 pages
    ISBN:9781450328937
    DOI:10.1145/2616498
    • General Chair:
    • Scott Lathrop,
    • Program Chair:
    • Jay Alameda
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

    In-Cooperation

    • NSF: National Science Foundation
    • Drexel University
    • Indiana University: Indiana University

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    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 13 July 2014

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    Author Tags

    1. Mothur
    2. Multi-threading
    3. OpenMP
    4. Shared Memory Architecture

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    XSEDE '14

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    XSEDE '14 Paper Acceptance Rate 80 of 120 submissions, 67%;
    Overall Acceptance Rate 129 of 190 submissions, 68%

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    Cited By

    View all
    • (2020)Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing DataFrontiers in Genetics10.3389/fgene.2020.60309311Online publication date: 30-Nov-2020

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