staramr
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Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
I assume the following traceback is due to the fact that there are no BLAST results. An improved error message could help here to guide the user ``` Traceback (most...
- Adds the ability to handle promoters (regions with both promoter nucleotide information and non-promoter codon information) - Adds handling of insertions and deletions in nucleotide and codon sequence -...
Dear @apetkau, I tried to implement some control about Pointfinder and staramr analysis. - [X] Check fasta file presence and overview list - [ ] Check fasta content depending of...
This is my code to check the pointfinder database before analysis, It read all fasta files, mutations lists and try to modify positions. It miss the control of indel and...
Only *salmonella* is supported from the PointFinder database. Add support for all other organisms - https://bitbucket.org/genomicepidemiology/pointfinder_db/src * [x] campylobacter * [ ] e.coli * [ ] gonorrhoeae * [ ]...
There is a request for an option to skip running MLST. Something along the lines of `--skip-mlst`.
Hi, I was wondering how I can update the databases used by the tool in Galaxy. Thank you!
Why unknown mutations are not found using PointFinder database? I would be very grateful if you can include this option too as it is the main reason I would like...
Set the --pointfinder-organism based on results of organism id instead of relying on the user to provide this information on the command-line.
Currently, right now we don't have have a predefined standard for how Staramr is maintained or how someone can contribute to this project. I propose implementing a contribution guide that...
