Journal Article

RESCRIPt: Reproducible sequence taxonomy reference database management

Robeson, Michael S., Bokulich, Nicholas A., Dillon, Matthew R., Foster, Jeffrey T., Kaehler, Benjamin D., Ziemski, Michal, O’Rourke, Devon R.

2021

Overview

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 .

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Animals / Biology and Life Sciences / Classification / Clustering / Computational Biology / Computer and Information Sciences / Database administration / Database Management Systems / Databases, Genetic - statistics & numerical data / Databases, Nucleic Acid / Deoxyribonucleic acid / Diet / DNA / DNA Barcoding, Taxonomic / DNA sequencing / Environmental DNA / Gene sequencing / Genes / Genetic engineering / Genomes / Genomics / Hepatitis / Humans / Metagenome / Metagenomics / Methods / Microbiomes / Microbiota - genetics / Nucleotide sequence / Nucleotide sequencing / Nucleotides / Phylogeny / Physical Sciences / Polls & surveys / Qualitative analysis / Quality standards / Reference materials / Reproducibility / Research and Analysis Methods / RNA, Ribosomal, 16S - genetics / Sequence Analysis / Software / Standardization / Taxonomy