Overview

Bruno Sobral, Shrinivasrao Mane, and Eric Nordberg gave invited presentations at a “Next Generation Sequencing: Transformative Technology for Biodiversity Science” workshop in Washington, DC on April 18-20, sponsored by the The Smithsonian Institution (SI), American Museum of Natural History (AMNH) and the Food and Drug Administration (FDA).  The purpose of the workshop was to invite software programmers who are actively working on NGS analysis software and pipelines to talk about integration of software for comparative genomics and metagenomics, including data input and outputs and future directions, to directly improve the software pipelines used at the FDA, USDA and CDC as well as others.  The PATRIC team members are participating in the Bioinformatic Software for Comparative Genomics and Metagenomics sections.  The discussion topics for software integration and future development include contig assembly and alignment, annotation and homology determination, phylogenomics, targeted resequencing, population genetics, metagenomics, and analysis of expression data (transcriptomes).

The PATRIC team gave three presentations entitled:

• PATRIC, Bacterial Resources, Web-Enabled Data/Analytical Capabilities and Challenges of Interoperability, Standardization, and Automation by Dr. Bruno Sobral.
• Workflows for Next-gen Sequence Analysis at VBI by Dr. Mane Shrinivasrao
• Phylogenomics at VBI by Eric Nordberg

Regarding the workshop, Dr. Sobral commented, “The opportunity to apply high-throughput data to the analysis of diversity as well as toward the mapping of phenotypic diversity to genetic diversity is enormously exciting scientifically and of great value to our understanding of the ecology of health, whether it be of our planet or our bodies.  The leadership of the organizations that brought together this meeting has provided a truly transdisciplinary nexus in which to discuss how to make such data accessible to a variety of communities in the most effective manner possible.  In the context of the PATRIC and Pathoge Portal projects, we can easily see how what we are going can be made of greatest relevance and utility to the constituencies present and are excited to be able to work with them more closely in the future to ensure that everything we build and deploy is also contributing to their interests and needs in the most effective and scalable manner possible.”