Using KBase to Assemble and Annotate Prokaryotic Genomes

Benjamin Allen1, Meghan Drake1, Nomi Harris2, Tarah Sullivan3

1 Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 2 Environmental Genomics & Systems Biology Group, Lawrence Berkeley National Laboratory, Berkeley, 3 Department of Crop and Soil Sciences, Washington State University, Pullman
Publication Name:  Current Protocols in Microbiology
Unit Number:  Unit 1E.13
DOI:  10.1002/cpmc.37
Online Posting Date:  August, 2017
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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. © 2017 by John Wiley & Sons, Inc.

Keywords: annotation; assembly; genomics; systems biology; KBase

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Quality Assessment and De Novo Assembly of Prokaryotic DNA Short Reads
  • Support Protocol 1: Using Narratives in KBase
  • Support Protocol 2: Uploading Short Reads to KBase from a Desktop Computer
  • Basic Protocol 2: Genome Annotation and Comparison of Annotations
  • Support Protocol 3: Downloading Data from KBase to a Desktop Computer
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Quality Assessment and De Novo Assembly of Prokaryotic DNA Short Reads

  Materials
  • An Internet‐accessible computer with a recent version Chrome, Firefox, or Safari
  • A KBase account. KBase is free to sign up for and use. All functionality detailed in this protocol requires being logged in with a KBase account: http://kbase.us/sign‐up‐for‐a‐kbase‐account/
  • Saved Narrative ( protocol 2)

Support Protocol 1: Using Narratives in KBase

  Materials
  • An Internet‐accessible computer with a recent version Chrome, Firefox, or Safari
  • A KBase account. KBase is free to sign up for and use. All functionality detailed in this protocol requires being logged in with a KBase account: http://kbase.us/sign‐up‐for‐a‐kbase‐account/

Support Protocol 2: Uploading Short Reads to KBase from a Desktop Computer

  Materials
  • An Internet‐accessible computer with a recent version Chrome, Firefox, or Safari
  • A KBase account. KBase is free to sign up for and use. All functionality detailed in this protocol requires being logged in with a KBase account: http://kbase.us/sign‐up‐for‐a‐kbase‐account/
  • Short reads from an Illumina sequencing platform in FASTQ format

Basic Protocol 2: Genome Annotation and Comparison of Annotations

  Materials
  • An Internet‐accessible computer with a recent version Chrome, Firefox, or Safari
  • A KBase account. KBase is free to sign up for and use. All functionality detailed in this protocol requires being logged in with a KBase account: http://kbase.us/sign‐up‐for‐a‐kbase‐account/

Support Protocol 3: Downloading Data from KBase to a Desktop Computer

  Materials
  • An Internet‐accessible computer with a recent version Chrome, Firefox, or Safari
  • A KBase account. KBase is free to sign up for and use. All functionality detailed in this protocol requires being logged in with a KBase account: http://kbase.us/sign‐up‐for‐a‐kbase‐account/
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Figures

Videos

Literature Cited

  Arkin, A. P., Stevens, R. L., Cottingham, R. W., Maslov, S., Henry, C. S., Dehal, P., … Yoo, S. (2016). The DOE systems biology knowledgebase (KBase). bioRxiv, https://doi.org/10.1101/096354.
  Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., … Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single‐cell sequencing. Journal of Computational Biology, 19(5), 455–477. doi: 10.1089/cmb.2012.0021.
  Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075. doi: 10.1093/bioinformatics/btt086.
  Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119. doi: 10.1186/1471‐2105‐11‐119.
  Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., … Stevens, R. (2014). The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Research, 42(D1), D206–D214. doi: 10.1093/nar/gkt1226.
  Scheuring, S., Nevo, R., Liu, L.‐N., Mangenot, S., Charuvi, D., Boudier, T., … Reich, Z. (2014). The architecture of Rhodobacter sphaeroides chromatophores. Biochimica et Biophysica Acta, 1837(8), 1263–1270. doi: 10.1016/j.bbabio.2014.03.011.
  Seemann, T. (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14), 2068–2069. doi: 10.1093/bioinformatics/btu153.
  Zerbino, D. R., & Birney, E. (2008). Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18(5), 821–829. doi: 10.1101/gr.074492.107.
Internet Resources
  https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  FastQC Resource.
  http://kbase.us
  KBase homepage.
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