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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Staramr M. tuberculosis integration? #112

Closed Takadonet closed 4 years ago

Takadonet commented 4 years ago

Hi,

This paper just came out with a new pointfinder database for M. tuberculosis:

"Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834686/pdf/fmicb-10-02464.pdf

Database: https://bitbucket.org/genomicepidemiology/pointfinder_db/src/master/mycobacterium_tuberculosis/

Staramr searches pointfinder databases, would it be possible to integrate this pointfinder database within staramr?

Thanks! Dan

dfornika commented 4 years ago

Typo in your database link above.

https://bitbucket.org/genomicepidemiology/pointfinder_db/src/master/mycobacterium_tuberculosis/

Takadonet commented 4 years ago

Thanks @dfornika

charlottecc commented 4 years ago

Hi,

Would it also be possible to integrate Staphylococcus aureus into the pointfinder database as well?

Thanks! Charlotte

Takadonet commented 4 years ago

Closing issue since moved requests into #17