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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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RESCRIPt: Reproducible sequence taxonomy reference database management.

Michael S Robeson1, Devon R O'Rourke2, Benjamin D Kaehler3

  • 1University of Arkansas for Medical Sciences, Department of Biomedical Informatics, Little Rock, Arkansas, United States of America.

Plos Computational Biology
|November 8, 2021
PubMed
Summary
This summary is machine-generated.

RESCRIPt software democratizes reference database creation for microbiome, eDNA, and genome studies. It enables reproducible generation and management of sequence databases, improving research transparency and comparability.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Nucleotide sequence and taxonomy reference databases are essential for microbiome analysis, metabarcoding, and environmental DNA (eDNA) surveys.
  • Generating, managing, and evaluating these databases present significant challenges, hindering reproducibility and cross-study comparisons due to varying database compositions.

Purpose of the Study:

  • To develop a robust software package (RESCRIPt) for reproducible generation and management of reference sequence taxonomy databases.
  • To provide tools for evaluating, comparing, and exploring characteristics of different reference databases.

Main Methods:

  • Developed RESCRIPt, a Python 3 software package and QIIME 2 plugin.
  • Implemented functions for streamlined database creation from popular sources.
  • Included functionalities for database evaluation, comparison, and interactive exploration.

Main Results:

  • Demonstrated RESCRIPt's utility with popular databases (SILVA, Greengenes, NCBI-RefSeq, GTDB, BOLD, GenBank) for various applications.
  • Showcased that database size is not the sole determinant of quality; standardized taxonomies and type strain focus offer advantages.
  • Found that curation (quality filtering) benefits databases, while sequence clustering can be detrimental.

Conclusions:

  • RESCRIPt empowers researchers to reproducibly and transparently create custom reference databases.
  • The software addresses bottlenecks in database management, enhancing the reliability of microbiome, eDNA, and genomic analyses.
  • RESCRIPt facilitates standardized and reproducible research workflows across diverse biological applications.