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

ABSTRACT: With the advent of next-generation whole-genome sequencing (WGS), the need for good-quality and well-characterised Salmonella genomes has increased over the past years. Good-quality complete genomes are often required for assembly reference mapping or phylogenetic single nucleotide polymorphism (SNP) analysis. Complete genomes or contigs from specific sources or serovars are also searched for clustering analysis or source attribution studies. Therefore, new bioinformatics tools are needed for the extraction of good-quality and well-characterised genomes from public databases. Here, we developed SalmoDEST, an open-source Python tool capable of extracting Salmonella genomes with a coverage higher than 50x and genome length over 4Mb from the GenBank database in the form of compl

SUBMITTER: Cherchame E 

PROVIDER: S-EPMC8874161 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature