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Bioinformatics Services Now Available at ISU CVM

The College of Veterinary Medicine (CVM) in collaboration with the Laurence H. Baker Center for Bioinformatics and Biological Statistics has assisted in purchasing two identical 24-node clusters for Next-Generation Sequencing (NGS) data analysis and molecular dynamics. Each computational node has two Intel six-core Xeon E5-2620 2.0 Ghz processors, 64 GB RAM, and 1 TB hard disk for scratch space for a total of 288 processors and 1536 GB RAM per cluster. Communication between the nodes relies on 1 GB networking for cluster management and FDR Infiniband (Fourteen Data Rate, 14Gb/s data rate per lane) for parallel computing. In addition to this capacity for massively parallel downstream analysis, we have dedicated hardware and personnel to update and maintain the server and keep the bioinformatic programs ‘cutting edge’. Moreover, the college has employed an ‘in-house’ bioinformaticist to assist CVM faculty, staff and students with design of NGS projects and their post-sequencing analyses. 

 

 

1. Pre-Project Consultation can encompass discussions of:

a. How much NGS sequencing data is necessary (depth of coverage, size of transcriptome, etc.) per organism;

b. Determining the most appropriate NGS sequencing platform for the type of data needed (i.e., will be be used for assembly, curation, gap closure, transcriptome, 16S rDNA, shotgun metagenomics, etc.?);

c. Creating a realistic project timeline;

d. Identifying the most appropriate sequencing facilities for the project duration, funding available and data requirements; and

e. Appropriate verbiage to support grant applications.

2. Library Construction Consultation could involve:

a. Determining which library preparations are appropriate for each NGS sequencing project;

b. Indexing options for sequencing multiple samples per sequencing run;

c. Providing advice on in-house preparation of libraries, their quantification and quality control and a cost/benefit analysis of outsourcing library preparation; and

d. Providing technical assistance for Illumina paired-end and mate-pair libraries.

3. Data Analysis encompasses:

a. Storage of raw and assembled data (storage dependent);

b. De-multiplexing (separating multiple libraries pooled in a single sequencing run);

c. Quality analysis (i.e., providing assistance in determining if one’s sequence data are of sufficient quality);

d. Genomic sequence assembly to obtain draft quality genomes using

i. ELAND v2 (CASAVA 1.8 pipeline)

ii. Velvet

iii. Newbler and

iv. Hybrid Assembly;

e. Optimized assembly for specific genomes using iterations of basic assemblers with modified parameters to optimize assembly outcome; and

f. Explanations as to why and how the data were assembled.

4. Dissemination of NGS knowledge will include holding seminars, providing consults and active participation in the VetMed NGS Users Group to improve bioinformatic and NGS knowledge in the CVM

 

 

If you interested in downstream analysis of data Paul can assist your lab. Please contact paulm@iastate.edu for more details.

 

 


 

 

There is a VetMed NGS Users Group meets the first of every month at 12 noon. Please email Paul or jbeetham@iastate.edu if you would like to know more.