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Title: Using KBase to Assemble and Annotate Prokaryotic Genomes

The DOE Systems Biology Knowledgebase is an open–access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next–Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes. As a result, this unit demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase that can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion.
Authors:
 [1] ; ORCiD logo [1] ;  [2] ;  [3]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Washington State Univ., Pullman, WA (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Current Protocols in Microbiology
Additional Journal Information:
Journal Volume: 46; Journal Issue: 1; Journal ID: ISSN 1934-8525
Publisher:
Wiley
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; annotation; assembly; genomics; systems biology; KBase
OSTI Identifier:
1462908

Allen, Benjamin H., Drake, Meghan M., Harris, Nomi, and Sullivan, Tarah. Using KBase to Assemble and Annotate Prokaryotic Genomes. United States: N. p., Web. doi:10.1002/cpmc.37.
Allen, Benjamin H., Drake, Meghan M., Harris, Nomi, & Sullivan, Tarah. Using KBase to Assemble and Annotate Prokaryotic Genomes. United States. doi:10.1002/cpmc.37.
Allen, Benjamin H., Drake, Meghan M., Harris, Nomi, and Sullivan, Tarah. 2017. "Using KBase to Assemble and Annotate Prokaryotic Genomes". United States. doi:10.1002/cpmc.37. https://www.osti.gov/servlets/purl/1462908.
@article{osti_1462908,
title = {Using KBase to Assemble and Annotate Prokaryotic Genomes},
author = {Allen, Benjamin H. and Drake, Meghan M. and Harris, Nomi and Sullivan, Tarah},
abstractNote = {The DOE Systems Biology Knowledgebase is an open–access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next–Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes. As a result, this unit demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase that can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion.},
doi = {10.1002/cpmc.37},
journal = {Current Protocols in Microbiology},
number = 1,
volume = 46,
place = {United States},
year = {2017},
month = {8}
}