Using KBase to assemble and annotate prokaryotic genomes

Benjamin Allen; Meghan Drake; Nomi Harris; Tarah Sullivan

doi:10.1002/cpmc.37

Using KBase to assemble and annotate prokaryotic genomes

Benjamin Allen, Meghan Drake, Nomi Harris, Tarah Sullivan

Computational and Predictive Biology

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) 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. 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.

Original language	English
Pages (from-to)	1E.13.1-1E.13.18
Journal	Current Protocols in Microbiology
Volume	2017
DOIs	https://doi.org/10.1002/cpmc.37
State	Published - Aug 1 2017

Funding

This manuscript has been co-authored by UT-Battelle, LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains, and the publisher, by accepting the article for publication, acknowledges, that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). This work is supported as part of the Genomic Sciences Program DOE Systems Biology Knowledgebase (KBase) funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231 (to Lawrence Berkeley National Laboratory), DE-AC02-06CH11357 (to Argonne National Laboratory), DE-AC05-00OR22725 (to Oak Ridge National Laboratory), and DE-AC02-98CH10886 (to Brookhaven National Laboratory).

Keywords

Annotation
Assembly
Genomics
KBase
Systems biology

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10.1002/cpmc.37

Cite this

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abstract = "The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) 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. 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.",

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AB - The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) 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. 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.

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Using KBase to assemble and annotate prokaryotic genomes

Abstract

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Keywords

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