> For the complete documentation index, see [llms.txt](https://kb.ezbiocloud.net/home/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples/sra-samples.md). # 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 (). ### 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. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples/sra-samples.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.