How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
Hi,
I am working on a project to determine antibiotic resistance origins in E. coli. We have amplified 7 housekeeping genes using PCR and sequenced the product on Nanopore MINIon. I would like to determine the MLST profile for each isolate. I have 1 run for a barcoded 96 well plate with each well with one isolate. basecalling and demultiplexing are already done. I am not being able to move further.
Thank you for the help
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Give the sequences to an MLST server or commandline tool on a per-sample/isolate basis.
The tool will specify the format it wants - probably a multifasta
To complement Joe's answer: here is a webserver: https://cge.food.dtu.dk/services/MLST/ and a commandline tool: https://github.com/tseemann/mlst