Torsten Seemann
Torsten Seemann
So you want the SAM lines where _either end_ has been soft clipped between 50-100 bp?
@miguelpmachado is it in PubMLST ?
If you use ``` mlst --legacy --scheme campylobacter *.fasta ``` it will give you what you need? Try phyloviz? http://www.phyloviz.net/ Or Geoburst? http://www.phyloviz.net/goeburst/
@mdphan I could probably add them, but I would need a consistent place to download the alleles and scheme files from, that doesn't require any logins. Do you know how...
If you can write a stand-alone script that uses no non-core libraries that creates a compatible MLST output folder, then yes.
On the face of it, this seems reasonable. I had considered adding `796?' where 796 was the closest ST available etc. Distinguishing Partial match and Novel allele is trickier than...
@eneasdecarvalho 1. that might be possible 2. you can't really have a header in regular output, because the scheme might not be the same for all the input files. if...
`ekidna` is alpha status, doens't even generate names yet. But yes, the plan was to use a dependency system like make so it does it in parallel.
Related to https://github.com/tseemann/ekidna/issues/3
Due to COVID i am 1 year behind on my bacterial software tools. I have a release ready to go with new databases, but many of the schemes have changed...