NDLI: Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight

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Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight

Content Provider	ACM Digital Library
Author	Blood, Philip D. Schatz, Michael C. Marcus, Shoshana
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.
Starting Page	1
Ending Page	6
Page Count	6
File Format	PDF
ISBN	9781450328937
DOI	10.1145/2616498.2616502
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-07-13
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Plant genomics High-performance computing Dna sequencing Genome assembly Ngs Data-intensive computing Shared memory
Content Type	Text
Resource Type	Article

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