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...
| Κύριοι συγγραφείς: | , , , , , , |
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| Μορφή: | Άρθρο |
| Γλώσσα: | English |
| Έκδοση: |
Public Library of Science (PLoS)
2021-11-01
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| Σειρά: | PLoS Computational Biology |
| Διαθέσιμο Online: | https://doi.org/10.1371/journal.pcbi.1009581 |
| _version_ | 1831696620433965056 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T13:16:41Z |
| format | Article |
| id | doaj.art-3b3ee68d2d0a49df902bccb26c1813c2 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-20T13:16:41Z |
| publishDate | 2021-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-3b3ee68d2d0a49df902bccb26c1813c22022-12-21T19:39:31ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-11-011711e100958110.1371/journal.pcbi.1009581RESCRIPt: Reproducible sequence taxonomy reference database management.Michael S RobesonDevon R O'RourkeBenjamin D KaehlerMichal ZiemskiMatthew R DillonJeffrey T FosterNicholas A BokulichNucleotide 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.https://doi.org/10.1371/journal.pcbi.1009581 |
| spellingShingle | 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. PLoS Computational Biology |
| title | 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_short | RESCRIPt: Reproducible sequence taxonomy reference database management. |
| title_sort | rescript reproducible sequence taxonomy reference database management |
| url | https://doi.org/10.1371/journal.pcbi.1009581 |
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