RESCRIPt

RESCRIPt: Reproducible Generation and Evaluation of Nucleotide Sequence and Taxonomy Databases

RESCRIPt enables reproducible generation, management, curation, standardization, and evaluation of DNA and RNA sequence reference databases with associated taxonomic annotations for marker-gene sequencing, metagenome sequencing, diet metabarcoding, environmental DNA (eDNA) surveys, and genome analysis.

Key Features:

• Reproducible Database Construction: Generates transparent and consistent nucleotide sequence and taxonomy reference databases from public repositories.
• Sequence and Taxonomy Management: Acquires, filters, curates, and organizes DNA/RNA sequences and taxonomic annotations.
• Standardized Taxonomy and Database Comparison: Standardizes taxonomic annotations and quantitatively compares reference databases to improve cross-study comparability.
• Quality Curation: Performs quality filtering, evaluates database composition, and assesses the impact of sequence clustering on reference database quality.
• Database Integration: Supports database generation and evaluation using SILVA, Greengenes, NCBI-RefSeq, GTDB, BOLD, and GenBank.
• Quantitative and Qualitative Evaluation: Computes metrics to assess taxonomic composition, sequence diversity, and database characteristics.

Scientific Applications:

• Microbiome and Genomic Research: Constructs and evaluates reference databases for microbiome profiling, global hepatitis genome comparisons, eDNA surveys, diet metabarcoding, and genome comparison workflows, including standardized taxonomies and type strain-focused analyses.

Methodology:

Implements dedicated functions to retrieve sequences and taxonomies from public databases, apply quality filtering and curation, standardize taxonomic annotations, compute quantitative composition metrics, and perform comparative analyses to generate reproducible, application-specific reference databases.