Torsten Seemann

icon indicating a website link https://tseemann.github.io/

icon company The University of Melbourne icon location Melbourne, AUSTRALIA icon location Bioinformatician, microbial genomics

Results 326 comments of Torsten Seemann

zero clipping at the beginning of the read

@avilella what does "start" mean in a SAM file? I think alignments are always begin..end with begin

Suggestion - allow a reference to be set

Ultimately it should noty matter what reference you use, because the SNPs it generates are "core" only. But that said, it could still be useful. This project is very early...

Suggestion - allow a reference to be set

It's important to realise `ekidna` is not a variant calling pipeline. It is an experiment to see how fast a SNP/alignment based phylogeny can be; to fit between sketch based...

Suggestion - allow a reference to be set

Ok, that's a good use case. Thank you!

Get MLST DB location from environmental variable

Yes, this could be useful in a pipeline setup.

Get MLST DB location from environmental variable

@andersgs do you want this to over-ride the `--blastdb` option? (the `--datadir` option will be removed in 3.x version as i can extract that info from the blast database and...