The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

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

doi:10.4056/sigs.651139

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

Journal Article · Tue Mar 30 00:00:00 EDT 2010 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.651139· OSTI ID:1628697

Tanenbaum, David M. ^[1]; Goll, Johannes ^[2]; Murphy, Sean ^[2]; Kumar, Prateek ^[3]; Zafar, Nikhat ^[2]; Thiagarajan, Mathangi ^[2]; Madupu, Ramana ^[2]; Davidsen, Tanja ^[2]; Kagan, Leonid ^[2]; Kravitz, Saul ^[2]; Rusch, Douglas B. ^[2]; Yooseph, Shibu ^[3]

J. Craig Venter Institute, Rockville, MD (United States); DOE/OSTI
J. Craig Venter Institute, Rockville, MD (United States)
J. Craig Venter Institute, San Diego, CA (United States)

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].

View Accepted Manuscript (DOE)

Research Organization:: Institute for Biological Energy Alternatives, Rockville, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FG02-02ER63453

OSTI ID:: 1628697

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 2 Vol. 2; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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