DOE JGI Metagenome Workflow
Alicia Clum, Marcel Huntemann, Brian Bushnell, Brian Foster, Bryce Foster, Simon Roux, Patrick Hajek, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Yuko Yoshinaga, Ronan C. O’Malley, R. Seshadri, Nikos C. Kyrpides, Emiley A. Eloe‐Fadrosh, I-Min A. Chen, Alex Copeland, Natalia Ivanova
Abstract
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 results of processing are provided in several standard formats, such as fasta and gff, and can be used for subsequent integration into the Integrated Microbial Genomes and Microbiomes (IMG/M) system where they can be compared to a comprehensive set of publicly available metagenomes. As of 30 July 2020, 7,155 JGI metagenomes have been processed by the DOE JGI Metagenome Workflow. Here, we present a metagenome workflow developed at the JGI that generates rich data in standard formats and has been optimized for downstream analyses ranging from assessment of the functional and taxonomic composition of microbial communities to genome-resolved metagenomics and the identification and characterization of novel taxa. This workflow is currently being used to analyze thousands of metagenomic data sets in a consistent and standardized manner.