[question]

[Kokejuli]

Hello!

Firstable, I would like to say that Bactopia is awesome and the way is constructed is incredible!

1. I am working on MLST analysis, and I would like to know if you are considering in incorporating the tool chewBACCA in bactopia-tools. I think is necesssary this tool if you want to create your own MLST schemas to perform a wgMLST analyses. I have known that this issue was commented here: [bactopia-tool] cgMLST and wgMLST #242 , but I wonder if you decided something about that.

2. Another question that I have, is related the way the current mlst works. I have read in the code (https://github.com/tseemann/mlst/blob/master/bin/mlst) that the BLAST to do the allele call is using the schema allele sequences as the database, but why? I have tried to do a cgMLST using a shceme with 1000 genes and just are called a few alleles, meanwhile, if I use the assembly genome as database and the allele sequences as query I got all the allele sequences. I have to add here, that obviously is a more time-consuming process in my way and that I have to filter the best alignment for each gene (many alleles aligned againstt he assembly genome).

Thank you so much for your time and if you want me to explain something better let me know :)

[rpetit3]

Hi @Kokejuli

Thank you very much for your kind words, please let me know if you have any ideas or bactopia gives you any issues!

2. Let's answer 2 first. I think the results you are seeing with mlst are expected and Torsten has recommended to avoid using mlst for cgMLST schemas. Instead recommends something like chewBBACA. Along with this Lee Katz had a similar experience.

3. cgMLST is a tough one, because one like you say its something that is useful and would be nice to have, but I've been hoping for some sort of standardization of the process and more readily available schema. I personally don't make use of cgMLST or wgMLST on a daily basis so I'm out of the loop, and might just need to do some research.

At the moment, if I were to include chewBACCA, you would have to bring your own schema, either creating your own or using one of Chewie's schemas. I personally do not know enough about the schema creation process to be able to say "this is a good schema" or " this is a bad schema".

If this is something you are interested in helping with, I'm open to making attempts in getting something like this added to Bactopia, haha I just need guidance!

I hope this helps, always open to feedback here, and thank you for the questions!
Robert