EToKi

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Good morning, I hope it is relevant here. Could EToKi be used to search for an AA motif in the EnteroBase db? Thank you in advance El

Norina28

With phylo.py, the core genome output doesn't match expectations. Assuming I'm correct in thinking that the .matrix is the right output. With my alignment and a threshold of 0.95, 4,800,000/5,000,000...

moorembioinfo

Various minor fixes

NigelDyer

Need documentation on cgMLST

1

I am taking some notes on how I ran cgMLST, and I hope you can add documentation for it. Create database: this took a very long time ```bash # Downloaded...

lskatz

Hi, I wanted to make EToKi more accessible. Relevant: #11 Therefore, I replaced usearch with blastp. Subsequently it has been containerized in the staph-b docker space. I have also attached...

lskatz

--install --path

1

Hi, could you clarify in the documentation which things I can put into `--path`? Like if I have the entire spades package downloaded, do I just run it with `--path...

lskatz

Hello, I installed EToKi and tried the example as showed in the README file but I got the following error. ./EToKi.py MLSTdb -i examples/Escherichia.Achtman.alleles.fasta -r examples/Escherichia.Achtman.references.fasta -d examples/Escherichia.Achtman.convert.tab 2020-07-29 20:45:04.997470...

theInnuendoProject

Make pip installable

1

It would be very helpful to be able to `pip3 install EnSuit`.

tseemann