mSystems (Jun 2021)
DOE JGI Metagenome Workflow
- Alicia Clum,
- Marcel Huntemann,
- Brian Bushnell,
- Brian Foster,
- Bryce Foster,
- Simon Roux,
- Patrick P. Hajek,
- Neha Varghese,
- Supratim Mukherjee,
- T. B. K. Reddy,
- Chris Daum,
- Yuko Yoshinaga,
- Ronan O’Malley,
- Rekha Seshadri,
- Nikos C. Kyrpides,
- Emiley A. Eloe-Fadrosh,
- I-Min A. Chen,
- Alex Copeland,
- Natalia N. Ivanova
Affiliations
- Alicia Clum
- ORCiD
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Marcel Huntemann
- ORCiD
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Brian Bushnell
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Brian Foster
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Bryce Foster
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Simon Roux
- ORCiD
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Patrick P. Hajek
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Supratim Mukherjee
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- T. B. K. Reddy
- ORCiD
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Ronan O’Malley
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Emiley A. Eloe-Fadrosh
- ORCiD
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- I-Min A. Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Alex Copeland
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Natalia N. Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- DOI
- https://doi.org/10.1128/mSystems.00804-20
- Journal volume & issue
-
Vol. 6,
no. 3
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.
