Next Generation Sequencing Analysis Pipelines Offered by CCR Collaborative Bioinformatics Resource

Authors

• D Wheeler
• F Elloumi
• P Jailwala
• B Kim
• J Lack
• M Cam

Abstract

The CCR Collaborative Bioinformatics Resource (CCBR) provides CCR researchers with bioinformatics assistance and collaborates with researchers over longer terms to further their research goals. The group offers on-site collaborative bioinformatics services to researchers at both Bethesda and Frederick campuses. The group has expertise in a broad range of bioinformatics topics with an emphasis on the analysis of the data generated via high throughput Next Generation Sequencing (NGS) technologies. In addition to advice and consultation on experimental design, CCBR analysts help with the downstream processing, analysis, and interpretation of the biological data produced by a wide variety of large-scale -omics technologies including Next-generation sequencing (ExomeSeq, RNASeq, ChIPSeq, whole genome sequencing), and microarrays. Working in close collaboration with both the CCR sequencing facility and the Genomics Technology Laboratory at ATRF, the CCBR team provides integrated project management starting from experimental design, choice of technology, data generation, data analysis, visualization, and leading up to publication of scientific results. In order to meet the needs of CCR researchers, the CCBR offers NGS sequence analysis pipelines that take advantage of the capabilities of parallel execution offered on the NIH Biowulf Linux cluster. Highlighted here are NGS sequence analysis pipelines for RNASeq, ExomeSeq and ChIPSeq data. In addition to the pipelines themselves CCBR makes available a program called Pipeliner which provides a GUI interface to the ExomeSeq pipeline and will provide similar interfaces to other CCBR pipelines in the near future. Pipeliner runs on the Biowulf cluster.

Scientific Focus Area: Computational Biology

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