DOE JGI Metagenome Workflow
DOE JGI Metagenome Workflow
About this item
Full title
Author / Creator
Clum, Alicia , Huntemann, Marcel , Bushnell, Brian , Foster, Brian , Foster, Bryce , Roux, Simon , Hajek, Patrick P. , Varghese, Neha , Mukherjee, Supratim , Reddy, T. B. 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. and Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Publisher
United States: American Society for Microbiology
Journal title
Language
English
Formats
Publication information
Publisher
United States: American Society for Microbiology
Subjects
More information
Scope and Contents
Contents
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning.
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...
Alternative Titles
Full title
DOE JGI Metagenome Workflow
Authors, Artists and Contributors
Author / Creator
Huntemann, Marcel
Bushnell, Brian
Foster, Brian
Foster, Bryce
Roux, Simon
Hajek, Patrick P.
Varghese, Neha
Mukherjee, Supratim
Reddy, T. B. 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.
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Identifiers
Primary Identifiers
Record Identifier
TN_cdi_doaj_primary_oai_doaj_org_article_06d53c16ba8d4db29707812c62731c25
Permalink
https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_doaj_primary_oai_doaj_org_article_06d53c16ba8d4db29707812c62731c25
Other Identifiers
ISSN
2379-5077
E-ISSN
2379-5077
DOI
10.1128/mSystems.00804-20
