Retrieving Good-Quality Salmonella Genomes From the GenBank Database Using a Python Tool, SalmoDEST

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Next-generation whole-genome sequencing (WGS) necessitates high-quality, well-characterized *Salmonella* genomes.
• Complete genomes are crucial for reference mapping, phylogenetic SNP analysis, and source attribution studies.
• Existing bioinformatics tools lack efficient methods for extracting specific *Salmonella* genomes from public databases.

Purpose of the Study:

• To develop an open-source Python tool, SalmoDEST, for extracting high-quality *Salmonella* genomes.
• To enable the retrieval of genomes with specific coverage and length criteria from GenBank.
• To verify serovar and identify multi-locus sequence type (MLST) profiles of extracted genomes.

Main Methods:

• Developed SalmoDEST, a Python-based bioinformatics tool.
• Implemented criteria for genome extraction: coverage >50x, length >4Mb.
• Validated SalmoDEST using *S. Typhi* genomes and worldwide bovine isolates.
• Verified serovar and MLST profiles for retrieved genomes.

Main Results:

• SalmoDEST successfully extracts *Salmonella* genomes meeting quality standards (coverage >50x, length >4Mb).
• The tool verifies serovar and identifies MLST profiles.
• A curated list of 239 high-quality complete *Salmonella* genomes across 123 serovars was generated.
• Validation confirmed SalmoDEST's efficacy in retrieving reliable genomic data.

Conclusions:

• SalmoDEST is an effective, user-friendly tool for accessing high-quality *Salmonella* genomes.
• The tool supports public health, food safety, and research laboratories.
• Facilitates routine extraction of complete genomes or contigs for various analyses.