Generating and Analyzing DNA Sequence Using Next-Generation Sequencing Technologies
2011 Annual Report
1a.Objectives (from AD-416)
The objective of this proposal is to optimally utilize the DNA sequencing and data analysis resources at USDA ARS Genomics and Bioinformatics Research Unit (GBRU) and Mississippi State University (MSU) through collaboration and utilization of complementary resources.
1b.Approach (from AD-416)
MSU researchers will provide DNA templates and reagents as required to generate DNA sequence data and perform down-stream computational analysis. MSU will provide computational resources to annotate and display genomic data sequencing.
USDA ARS GBRU will provide DNA sequencing services at cost with projects being approved on a case-by-case basis on species of interest to both parties.
All of these activities will be considered true collaborations and thus, by definition, each party will be considered to have provided a true intellectual contribution consistent with authorship.
The project is to leverage the DNA sequencing capacity of the ARS unit with the bioinformatic capabilities of Mississippi State University. This agreement enables the Catfish Genetics Research Unit, Stoneville, MS, to access a new bioinformatic computer to run the DNA assembly program called ABySS to assemble genomic DNA sequences of catfish. Previous attempts on the Amazon Cloud to assemble the catfish genome had failed due to limited random access memory (RAM) per computation node. This has allowed for advances in the catfish genome assembly at no cost to ARS in Stoneville, MS.
Participants met during the year to discuss computational needs of the MSA. Occasional phone conversations take place.