The JCVI Standard Operating Procedure for Annotating Prokaryotic Metagenomic Shotgun Sequencing Data

David Tanenbaum, Johannes Goll, Sean Murphy, Prateek Kumar, Nikhat Zafar, Mathangi Thiagarajan, Ramana Madupu, Tanja Davidsen, Leonid Kagan, Saul Kravitz, Douglas B. Rusch, Shibu Yooseph

Abstract


The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms.  The process can be equally applied to individual sequence reads from traditional Sanger capillary electrophoresis sequences, newer technologies such as 454 pyrosequencing, or sequence assemblies derived from one or more of these data types.  It includes the analysis of both coding and non-coding genes, whether full-length or, as is often the case for shotgun metagenomics, fragmentary.  The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation value hierarchy established through extensive manual curation.  The functional annotation attributes assigned by this system include gene name, gene symbol, GO terms [1], EC numbers [2], and JCVI functional role categories [3].

doi:10.4056/sigs.651139


Keywords


J. Craig Venter Institute, prokaryotic shotgun metagenomics, environmental sequencing, functional annotation, Global Ocean Sampling, Sargasso Sea

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Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

SIGS was founded with grants from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707. The journal became self-supporting on October 1, 2011.

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