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

doi:10.1093/bioinformatics/btaa277

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 journal › Article › peer-review

34 Scopus citations

Abstract

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.

AVAILABILITY AND IMPLEMENTATION: https://github.com/knights-lab/SHOGUN.

Original language	English (US)
Pages (from-to)	4088-4090
Number of pages	3
Journal	Bioinformatics
Volume	36
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btaa277
State	Published - Jul 1 2020

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

Keywords

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

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abstract = "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.AVAILABILITY AND IMPLEMENTATION: https://github.com/knights-lab/SHOGUN.",

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AU - Al-Ghalith, Gabriel A.

AU - Shields-Cutler, Robin R.

AU - Zhu, Qiyun

AU - Knight, Rob

AU - Knights, Dan

PY - 2020/7/1

Y1 - 2020/7/1

N2 - 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.AVAILABILITY AND IMPLEMENTATION: https://github.com/knights-lab/SHOGUN.

AB - 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.AVAILABILITY AND IMPLEMENTATION: https://github.com/knights-lab/SHOGUN.

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KW - Data Analysis

KW - Metagenomics

KW - Microbiota/genetics

KW - Software

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

Abstract

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Keywords

PubMed: MeSH publication types

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