How To
These are links to demonstrate how to access the NCBI Pathogen Detection data for some of the analysis tasks you might want to do. For more details see our documentation. The How To's are meant to demonstrate techniques to access the data avaliable and should be generalizable to answer other questions. If you have suggestions for changes or other How To's you think would be useful please set us know at pd-help@ncbi.nlm.nih.gov.
Visual How Tos
- How To: Find an isolate you submitted (.pptx)
- How To: Find the latest Salmonella in the Isolates Browser (.pptx)
- How To: Download a list of human, clinical E. faecailis isolates (.pptx)
- How To: Identify isolates in the same SNP cluster that share a set of genes (.pptx)
- How To: Download a list of all carbapenem resistance genes and point mutations from the Reference Gene Catalog (.pptx)
- How To: Download all the reference sequences for a set of proteins (.pptx)
- How To: Find all the known resistance mechanisms to a given drug (.pptx)
- How To: Download the nucleotide sequence of all MCR-1 alleles (.pptx)
- How To: Identify all the contigs that share a set of genes (.pptx)
- How To: Identify isolates that have a pair of genes on the same contig (.pptx)
- How To: Download a MicroBIGG-E table > 100,000 rows (all CARBAPENEM genes found in Pathogen Detection isolate assemblies) (.pptx)
- How To: Cite the Pathogen Detection Resource and the Data Contained Within (.pptx)
- How To: Identify carbapenem-resistant isolates without common acquired carbapenem resistance genes (.pptx)
- How To: Find, using the MicroBIGG-E Map, blaKPC-containing Klebsiella pneumoniae isolates from China and the U.S. in the Isolates Browser (.pptx)
- How To: Download, using the MicroBIGG-E Map, blaKPC nucleotide sequences from Klebsiella pneumoniae isolates from China and the U.S. (.pptx)
Other How Tos
- Isolates Browser How To: Quick link searches
- Isolates Browser How To: General text searches
- Isolates Browser How To: Field-specific searches
- Isolates Browser How To: Use filters to focus search results
- Isolates Browser How To: Identify the possible source of an outbreak
- How to submit data
- How to submit new beta-lactamase alleles