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

Full Text: HTML PDF

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

This article doi:10.4056/sigs.651139 has been cited by 13 other articles:

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
Allen et al.
ISME J 6(7) 1403.
10.1038/ismej.2011.201

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer
Ishii et al.
Nat Comms 4() 1601.
10.1038/ncomms2615

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
Lorenzi et al.
Stand. Genomic Sci. 4(3) 418.
10.4056/sigs.1694706

High throughput sequencing methods for microbiome profiling: application to food animal systems
Highlander
Anim. Health. Res. Rev. 13(01) 40.
10.1017/S1466252312000126

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
Kim et al.
Genomics Inform 11(3) 102.
10.5808/GI.2013.11.3.102

The State of Standards in Genomic Sciences
Garrity
Stand. Genomic Sci. 5(3) 262.
10.4056/sigs.2515706

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
Chitsaz et al.
Nat Biotechnol 29(10) 915.
10.1038/nbt.1966

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential
Klatt et al.
ISME J 5(8) 1262.
10.1038/ismej.2011.73

Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters
Hugoni et al.
Proceedings of the National Academy of Sciences 110(15) 6004.
10.1073/pnas.1216863110

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
Trimble et al.
BMC Bioinformatics 13(1) 183.
10.1186/1471-2105-13-183

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
Edlund et al.
Microbiome 1(1) 25.
10.1186/2049-2618-1-25

Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa
Rusch et al.
Genome Announcements 1(1) e00030-12.
10.1128/genomeA.00030-12

Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary
Marsan et al.
Genome Announcements 2(1) e01111-13.
10.1128/genomeA.01111-13




Announcement

Publication of Standards in Genomic Sciences has been transferred to a new publisher, BioMed Central on behalf of the Genomic Standards Consortium. All submissions to the journal should now be made directly through the BMC website for the journal at: http://www.standardsingenomics.com

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.

Standards in Genomic Sciences is indexed in: