SampleMiner

SampleMiner (SM) is a Python script that helps researchers dependent on limited internet resources to locally perform microbial isolates sampling, metadata retrieval and whole-genome sequences (WGS) download, provided the metadata pages of the online database can be downloaded as comma-separated value files. SM allows for the inclusion of individuals in a sample based on keywords, followed by easy deletion of all isolates that match exclusion criteria. Finally, SM allows for easy download of all retrievable WGS of isolates via one-time access to NCBI. So far, Enterobase and Patric derived metadata importation into local databases have been implemented into SM.