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Bioinformatics Shared Resources
Sanford Burnham Prebys Medical Discovery Institute
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NEXT-GEN SEQUENCING DATA ANALYSIS
We have paper published about finding
mutations causing CHIME syndrome:
Ng BG, Hackmann K, Jones MA,
, He P,
Bhide S, Cantagrel V, Gleeson JG, Paller AS, Schnur RE, Tinschert S, Zunich J, Hegde MR, Freeze HH. .Mutations in the Glycosylphosphatidylinositol Gene PIGL Cause CHIME Syndrome.Am J Hum Genet. 2012, 90(4):685-8.
Resources for analysis
For analysis of next generation DNA sequence data generated on the AB SOLiD 4 sequencer, there are two 5 node Linux clusters. Next-Gen data analysis tools include BioScope, Avadis NGS, Broad Institute Genome Analysis ToolKit (GATK), SOLiD Alignment Browser (SAB), SOLiD Analysis Tools (SAT), and Partek tools. BioScope software provides a command line and simple web interface for running application-specific sequence analysis tools. These tools allow configurable workflows for resequencing and whole transcriptome analysis and ChIP-seq analysis.
SBMRI has SOLID and
platforms. Through our collaborators we have access to (and already performed data analysis) Illunima platform.
Workflows and Pipelines
For one of the project we developed and optimized the following data analysis pipeline (numbers shown are approximate and varied from project to project).