SHOGUN: A modular, accurate and scalable framework for microbiome quantification

Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knights

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


SUMMARY: The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research.


Original languageEnglish (US)
Pages (from-to)4088-4090
Number of pages3
Issue number13
StatePublished - Jul 1 2020

Bibliographical note

Funding Information:
This work was supported by the University of Minnesota Masonic Cancer Center (to D.K.), National Institutes of Health grant R01AI121383 (to D.K.), grant P01DK078669 and in-kind support from National Science Foundation 1565057 and the Alfred P. Sloan Foundation 2017–9838 (to R.K., QIIME and QIITA) and by the Masonic Cancer Center at the University of Minnesota.

Publisher Copyright:
© 2020 The Author(s). Published by Oxford University Press. All rights reserved.


  • Bayes Theorem
  • Data Analysis
  • Metagenomics
  • Microbiota/genetics
  • Software

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Journal Article
  • Research Support, N.I.H., Extramural


Dive into the research topics of 'SHOGUN: A modular, accurate and scalable framework for microbiome quantification'. Together they form a unique fingerprint.

Cite this