Large-scale sequencing and assembly of cereal genomes using blacklight

Blood, P. D., Marcus, S., Schatz, M. C. (July 2014) Large-scale sequencing and assembly of cereal genomes using blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment. Article number 20.

URL: http://dl.acm.org/citation.cfm?id=2616502
DOI: 10.1145/2616498.2616502D

Abstract

Wheat, corn, and rice provide 60 percent of the world's food intake every day, and just 15 plant species make up 90 percent of the world's food intake. As such there is tremendous agricultural and scientific interest to sequence and study plant genomes, especially to develop a reference sequence to direct plant breeding or to identify functional elements. DNA sequencing technologies can now generate sequence data for large genomes at low cost, however, it remains a substantial computational challenge to assemble the short sequencing reads into their complete genome sequences. Even one of the simpler ancestral species of wheat, Aegilops tauschii, has a genome size of 4.36 gigabasepairs (Gbp), nearly fifty percent larger than the human genome. Assembling a genome this size requires computational resources, especially RAM to store the large assembly graph, out of reach for most institutions. In this paper, we describe a collaborative effort between Cold Spring Harbor Laboratory and the Pittsburgh Supercomputing Center to assemble large, complex cereal genomes starting with Ae. tauschii, using the XSEDE shared memory supercomputer Blacklight. We expect these experiences using Blacklight to provide a case study and computational protocol for other genomics communities to leverage this or similar resources for assembly of other significant genomes of interest. Copyright 2014 ACM.

Item Type: Paper
Additional Information: Meeting abstract
Uncontrolled Keywords: Data-intensive computing DNA sequencing Genome assembly High-performance computing NGS Plant genomics Shared memory
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
Publication Type > Meeting Abstract
Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: Matt Covey
Date: 13 July 2014
Date Deposited: 22 Aug 2014 20:59
Last Modified: 06 Feb 2018 16:04
URI: http://repository.cshl.edu/id/eprint/30718

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