Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome

Loading...
Thumbnail Image
Can’t use the file because of accessibility barriers? Contact us with the title of the item, permanent link, and specifics of your accommodation need.

Date

2015-07-26

Journal Title

Journal ISSN

Volume Title

Publisher

ACM, New York, NY

Abstract

Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.

Description

This paper was presented at XSEDE 15 conference.

Keywords

NCGAS, Bioinformatics, Genome Analysis, Transcriptome, Sequence Assembly, Pine, large memory, Conifer, HPC

Citation

Le-Shin Wu, Carrie L. Ganote, Thomas G. Doak, William Barnett, Keithanne Mockaitis, and Craig A. Stewart. 2015. Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome. In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure (XSEDE '15). ACM, New York, NY, USA. DOI=http://dx.doi.org/10.1145/2792745.2792748

DOI

Link(s) to data and video for this item

Relation

Rights

Except where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This content is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). 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

Type

Article