16s_clc
Cross-Laboratory Comparison of Bacterial 16S rRNA Communities in Soil Using Nanopore Sequencing
Science Score: 67.0%
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✓codemeta.json file
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✓.zenodo.json file
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Found 1 DOI reference(s) in README -
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Low similarity (5.0%) to scientific vocabulary
Repository
Cross-Laboratory Comparison of Bacterial 16S rRNA Communities in Soil Using Nanopore Sequencing
Basic Info
- Host: GitHub
- Owner: DanielManter-USDA
- License: gpl-3.0
- Default Branch: main
- Size: 10.5 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
Unveiling Errors in Soil Microbial Community Sequencing: A Case for Reference Soils and Improved Diagnostics for Nanopore Sequencing
Daniel K. Manter, Catherine L. Reardon, Amanda J. Ashworth, Abasiofiok M. Ibekwe, R. Michael Lehman, Jude E. Maul, Daniel N. Miller, Timothy Creed, Patrick M. Ewing, Stanley Park, Thomas F. Ducey, Heather L. Tyler, Kristen S. Veum, Sharon L. Weyers, David B. Knaebel
Communications Biology DOI: TBD
Sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and inclusion of a reference soil can help ensure data validity and facilitate comparison of multiple sequencing runs within and between laboratories.
Owner
- Name: Daniel Manter
- Login: DanielManter-USDA
- Kind: user
- Company: @USDA-REE-ARS
- Repositories: 1
- Profile: https://github.com/DanielManter-USDA
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Manter
given-names: Daniel
orcid: https://orcid.org/0000-0001-7729-7197
- family-names: Reardon
given-names: Catherine
orcid: https://orcid.org/0000-0002-2195-1214
- family-names: Ashworth
given-names: Amanda
- family-names: Ibekwe
given-names: Abasiofiok
- family-names: Lehman
given-names: Michael
- family-names: Maul
given-names: Jude
- family-names: Miller
given-names: Daniel
- family-names: Creed
given-names: Timothy
- family-names: Ewing
given-names: Patrick
- family-names: Park
given-names: Stanley
- family-names: Ducey
given-names: Thomas
- family-names: Tyler
given-names: Heather
- family-names: Veum
given-names: Kristen
- family-names: Weyers
given-names: Sharon
- family-names: Knaebel
given-names: David
title: Cross-Laboratory Comparison of Bacterial 16S rRNA Communities in Soil Using Nanopore Sequencing
version: v.1.0
identifiers:
- type: doi
value: 10.5281/zenodo.11557861
date-released: 2024-06-07