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RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

View ORCID ProfileMichael S. Robeson II, View ORCID ProfileDevon R. O’Rourke, View ORCID ProfileBenjamin D. Kaehler, View ORCID ProfileMichal Ziemski, View ORCID ProfileMatthew R. Dillon, View ORCID ProfileJeffrey T. Foster, View ORCID ProfileNicholas A. Bokulich
doi: https://doi.org/10.1101/2020.10.05.326504
Michael S. Robeson II
1University of Arkansas for Biomedical Sciences, Department of Biomedical Informatics, Little Rock, AR, USA
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Devon R. O’Rourke
2Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Benjamin D. Kaehler
3School of Science, University of New South Wales, Canberra, Australia
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Michal Ziemski
4Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland
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Matthew R. Dillon
2Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Jeffrey T. Foster
2Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
5Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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Nicholas A. Bokulich
4Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland
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  • ORCID record for Nicholas A. Bokulich
  • For correspondence: nicholas.bokulich@hest.ethz.ch
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Abstract

Background Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardizations limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a software package for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases.

Results To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA, and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes.

Conclusions RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/bokulich-lab/RESCRIPt

  • https://doi.org/10.5281/zenodo.3891931

  • https://github.com/bokulich-lab/db-benchmarks-2020

  • https://github.com/devonorourke/COIdatabases

  • https://github.com/mikerobeson/q2-sourmash/tree/use-fasta

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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RESCRIPt: Reproducible sequence taxonomy reference database management for the masses
Michael S. Robeson II, Devon R. O’Rourke, Benjamin D. Kaehler, Michal Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich
bioRxiv 2020.10.05.326504; doi: https://doi.org/10.1101/2020.10.05.326504
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RESCRIPt: Reproducible sequence taxonomy reference database management for the masses
Michael S. Robeson II, Devon R. O’Rourke, Benjamin D. Kaehler, Michal Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich
bioRxiv 2020.10.05.326504; doi: https://doi.org/10.1101/2020.10.05.326504

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