O157 Lineage Assignment

A script that returns the Lineage-Specific Polymorphism Assay-6 (LSPA-6) result for O157 Escherichia coli when given genomic data in a FASTA format.

The LSPA-6 lineage typing is based on:

Yang Z, Kovar J, Kim J, Nietfeldt J, Smith DR, Moxley RA, Olson ME, Fey PD, Benson AK. 2004. Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples. Appl Environ Microbiol 70:6846-54.

Assumptions

• If you are a USDA user with access, this program runs natively on CERES as of 7/1/2020.
• Python is installed on machine.
• User has bash terminal.

Input

• Open Terminal
• Call program
• ./LSPA6Long.sh [output CSV File Name] [Fasta File(s)]

Output

• A .csv file will be created containing concise information about each strain or contig (as separated by >).

  • Unless directed to a different location, the output CSV file will be created wherever the script is located. The .csv file can be opened by Microsoft Excel.
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• Verbose output on the screen is also an output. This output can be sent to a file.

  • This may be useful to inspect where the primers could potentially bind in the genome.

  • ./LSPA6Long.sh [output CSV File Name] [Fasta File(s)] > Information.txt

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• Please note that LSPA-6 results other than 111111, 211111, and 222222 will be assigned the lineage of "manually assign". Please examine these genomes with greater scrutiny.