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bvalot / pyMLST

whole genome MLST analysis
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Create a database input example #9

Closed sunx0766 closed 1 year ago

sunx0766 commented 1 year ago

Hi there!

Thank you so much for developing this tool for MLST. I'm excited in using this tool for wgMLST however running into some problems while creating my own database for Streptococcus agalactiae. I was able to obtain the different allels from pubMLST in a multi-fasta format for each gene, and there are around ~1400 genes I'm interested in using for typing. How can I have the ~1400 multi-fasta files as my input? Would you be willing to provide an example of what the create database command look like? Thank you!

bvalot commented 1 year ago

Hello,

The most easy way to create a cg/wgMLST database for a new species is to use a annotated genome. For you species, you can use this genome

You need to download genes of this genome for input of wgMLST: Clic on Send to -> coding sequence -> FASTA nucleotide

You use this multi-fasta as input of wgMLST create and you need to add the -r option

Hope it would be help, Benoit

sunx0766 commented 1 year ago

Hi Benoit,

Thank you so much, this clarified things up and worked!

Kind regards, Erica