Torsten Seemann

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

icon company The University of Melbourne icon location Melbourne, AUSTRALIA icon location Bioinformatics and genomics for public health and clinical microbiology

Results 439 comments of Torsten Seemann

Useful enhancements

@JA-Lacey can you please break this into separate issues and assign Krsity and label as Enhancement. and then close this issue?

bedtools intersect fails when GFF file contains a ##FASTA section

It's not 100% clear from the GFF3 spec if you can **not** have the `##FASTA` section and still put `>fasta` sequences at the end anyway. I've seen files like that....

Fixed: updating NCBI database

Was fixed.

`--proteins` external database doesn't give excpected assignements

@fconstancias your file looks good are they short hits? prokka needs 80% coverage minimum

stats in machine readable format?

Thank you

fix full.aln to have correct VARIANT count when running snippy-core

@hsnguyen I am sorry i never looked at my PRs since COVID. Your work is good, but I think we can now use https://github.com/rrwick/Core-SNP-filter to do this.

Get genome size without temporary files

Could also use `ska2 cov R1 R2` for this, as well as smarter min-cov

Select multiple annotation modes?

THis is a good idea, common request. Is this for metagenomes?

No annotation of existing genes

Why did you use `--metagenome` ? Whem I run prokka on your genome I get 2,500 proteins. Which gene did it not find?

option to include scores in prokka output

You are right, prokka is vague about how it assigns its gene annotations. Theoretically it could be done, but I think `bakta` is a better choice now for genome annotation....