DOE JGI Metagenome Workflow

Clum, Alicia; Huntemann, Marcel; Bushnell, Brian; Foster, Brian; Foster, Bryce; Roux, Simon; Hajek, Patrick P.; Varghese, Neha; Mukherjee, Supratim; Reddy, T. K.; Daum, Chris; Yoshinaga, Yuko; O’Malley, Ronan; Seshadri, Rekha; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.; Chen, I-Min A.; Copeland, Alex; Ivanova, Natalia N.

doi:10.1128/msystems.00804-20

DOE JGI Metagenome Workflow

Journal Article · Tue May 18 00:00:00 EDT 2021 · mSystems

DOI:https://doi.org/10.1128/msystems.00804-20· OSTI ID:1826557

^[1]; ^[1]; Bushnell, Brian ^[1]; Foster, Brian ^[1]; Foster, Bryce ^[1]; ^[1]; Hajek, Patrick P. ^[1]; Varghese, Neha ^[1]; Mukherjee, Supratim ^[1]; ^[1]; Daum, Chris ^[1]; Yoshinaga, Yuko ^[1]; O’Malley, Ronan ^[1]; Seshadri, Rekha ^[1]; Kyrpides, Nikos C. ^[1]; ^[1]; Chen, I-Min A. ^[1]; Copeland, Alex ^[1]; Ivanova, Natalia N. ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983).

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: U.S. Department of Energy; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1826557

Alternate ID(s):: OSTI ID: 1828334

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 3 Vol. 6; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
IMG
JGI
SOP
annotation
assembly
binning
metagenomics

DOE JGI Metagenome Workflow

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