SRA Samples

Imagine you find an isolate uploaded onto NCBI’s SRA that you suspect has been mislabelled. Downloading the sample from the SRA and uploading it to EzBioCloud's Genome Identification tool can help us find the species down to its strain level and place it on a phylogenetic tree to scrutinise its closely related neighbours.

Below, we will look at a case example of searching and preparing a Salmonella enterica isolate genome sample for upload to EzBioCloud Genome Identification.

Access NCBI SRA

Visit the NCBI SRA website (https://www.ncbi.nlm.nih.gov/sra).

Search for Salmonella enterica Infection

Use keywords like "Salmonella enterica infection" or more specific terms related to the infection along with "SRA" in the search bar to find relevant sequencing data.

Filter Results

Utilize filters such as organism name (Salmonella enterica), disease condition, sample type, or any associated keywords related to the infection to refine the search results.

Evaluate Metadata

Review the metadata of the identified runs to ensure they correspond to Salmonella enterica infections and match your research requirements.

Select Relevant Runs

Choose the sequencing runs that best suit your research objectives, ensuring they align with the specific strain or subtype of Salmonella enterica you are interested in.

Download Selected Data

Use tools such as the SRA Toolkit or the NCBI SRA Run Selector to download the selected sequencing data in FASTQ format.