Using KBase to Assemble and Annotate Prokaryotic Genomes

Allen, Benjamin H.; Drake, Meghan M.; Harris, Nomi; Sullivan, Tarah

doi:10.1002/cpmc.37

Title: Using KBase to Assemble and Annotate Prokaryotic Genomes

Journal Article · Tue Aug 15 00:00:00 EDT 2017 · Current Protocols in Microbiology

DOI:https://doi.org/10.1002/cpmc.37· OSTI ID:1462908

Allen, Benjamin H. ^[1];

^[1]; Harris, Nomi ^[2]; Sullivan, Tarah ^[3]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Washington State Univ., Pullman, WA (United States)

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.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1462908

Journal Information:: Current Protocols in Microbiology, Vol. 46, Issue 1; ISSN 1934-8525

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (9)

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Cited By (3)

Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards Lewis, Ricky W.; Islam, Anjuman; Opdahl, Lee Microbial Ecology, Vol. 78, Issue 3 https://doi.org/10.1007/s00248-019-01324-8	journal	February 2019
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms Whitmore, Leanne S.; Nguyen, Bernard; Pinar, Ali BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3025-9	journal	September 2019
Make the Most Out of Genome Announcements with KBase Allen, Benjamin; Land, Miriam; Wood-Charlson, Elisha Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); DOE Systems Biology Knowledgebase (KBase) https://doi.org/10.25982/1608940	dataset	January 2020

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