[bactopia-tool] cgMLST and wgMLST

[lskatz]

Related To

• [ ] Bactopia
• [x] Bactopia Tools

Is this related to a problem?

Now that we have core genome MLST (cgMLST) and whole genome MLST (wgMLST) methods out there, it would be amazing to include some workflow for analyzing these large schemes.

Is this something you would like to see added?

I would love to see a new cgMLST tool in Bactopia that works on genome assemblies.

Describe the solution you'd like

I have made a small survey of assembly-based methods and have come to the conclusion that ChewBBACA is probably the software of choice. Even in Torsten's MLST issues, he recommends ChewBBACA as the cgMLST method of choice.

Additional Information

There are the options for assembly free methods but given the overall workflow of bactopia, I would recommend assembly-based. Additionally, the assembly based methods have the advantage of calling new alleles which is sorely needed.

basic operations should be:

• download database from chewbbaca.online
• call alleles
• report - summary
• report - long form

[shlomobl]

Hi,

First of all thanks for putting all these tools together. I've been using many of them but having everything within a single pipeline is nice!

For pangenomes I suggest to take a look at PEPPAN (https://github.com/zheminzhou/PEPPAN).

I don't have experience with this pipeline but I'm about to use it. From what I've been reading, though, most of other pangenome pipelines target single species whereas PEPPAN looks to be well fit for multiple species (genus level), which is what I am working on.

[rpetit3]

With Bactopia v2, I can totally do this! I've started another issue here: https://github.com/bactopia/bactopia/issues/256

Thank you very much for the suggestion