RESCRIPt: Reproducible sequence taxonomy reference database management.

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 nucleoti...

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Autores principales:	Michael S Robeson, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/3b3ee68d2d0a49df902bccb26c1813c2
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spelling	oai:doaj.org-article:3b3ee68d2d0a49df902bccb26c1813c22021-12-02T19:57:58ZRESCRIPt: Reproducible sequence taxonomy reference database management.1553-734X1553-735810.1371/journal.pcbi.1009581https://doaj.org/article/3b3ee68d2d0a49df902bccb26c1813c22021-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009581https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Nucleotide 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 standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin 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. 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. 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.Michael S RobesonDevon R O'RourkeBenjamin D KaehlerMichal ZiemskiMatthew R DillonJeffrey T FosterNicholas A BokulichPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 11, p e1009581 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Michael S Robeson Devon R O'Rourke Benjamin D Kaehler Michal Ziemski Matthew R Dillon Jeffrey T Foster Nicholas A Bokulich RESCRIPt: Reproducible sequence taxonomy reference database management.
description	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 standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin 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. 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. 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.
format	article
author	Michael S Robeson Devon R O'Rourke Benjamin D Kaehler Michal Ziemski Matthew R Dillon Jeffrey T Foster Nicholas A Bokulich
author_facet	Michael S Robeson Devon R O'Rourke Benjamin D Kaehler Michal Ziemski Matthew R Dillon Jeffrey T Foster Nicholas A Bokulich
author_sort	Michael S Robeson
title	RESCRIPt: Reproducible sequence taxonomy reference database management.
title_short	RESCRIPt: Reproducible sequence taxonomy reference database management.
title_full	RESCRIPt: Reproducible sequence taxonomy reference database management.
title_fullStr	RESCRIPt: Reproducible sequence taxonomy reference database management.
title_full_unstemmed	RESCRIPt: Reproducible sequence taxonomy reference database management.
title_sort	rescript: reproducible sequence taxonomy reference database management.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/3b3ee68d2d0a49df902bccb26c1813c2
work_keys_str_mv	AT michaelsrobeson rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT devonrorourke rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT benjamindkaehler rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT michalziemski rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT matthewrdillon rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT jeffreytfoster rescriptreproduciblesequencetaxonomyreferencedatabasemanagement AT nicholasabokulich rescriptreproduciblesequencetaxonomyreferencedatabasemanagement
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RESCRIPt: Reproducible sequence taxonomy reference database management.

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