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Mykrobe-tools / mykrobe

Antibiotic resistance prediction in minutes
MIT License
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Mykrobe version v0.8.1 does not work with Staph. aureus? #91

Open davidjstudholme opened 4 years ago

davidjstudholme commented 4 years ago

Dear Mykrobe team,

according to your paper (Bradley et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 2015 6:10063), Mykrobe should be able to deal with Staph. aureus genomic data. However, when I attempt to analyse data from SRA acccession ERR1212590, I get the following error message from Mykrobe:

"This sample does not appear to contain any Mycobacterial data (or it is amplicon data, which is not supported), and therefore the predictor does not give susceptibility predictions".

I recall that previous versions of Mykrobe came in two flavours: one for Staph. and one for TB. I could not find a Staph. flavour download on your website.

According to the 'About' tab, I am using: Predictor version v0.8.0-draft · Desktop app version v0.8.1 on Mac.

Is there a way of running this version on Mac in 'Staph. mode' or has this functionality been removed?

Best wishes,

David

iqbal-lab commented 4 years ago

Hi David Many apologies - you need a separate app for staph, which we failed to release in the last releas,e which was attached to the TB paper. We will escalate this issue and get back to you with a time estimate for the staph app release

mbhall88 commented 4 years ago

In the meantime, if you are able to use the command-line version of Mykrobe this supports Staph if you install from my fork (waiting for #89 to be merged and then this will be in a new release).

davidjstudholme commented 4 years ago

Thank you very much indeed. Since we are using this in the context of a student workshop I would prefer to stick with the GUI only. Our main focus is on Tb rather than Staph.

We did find some other discrepancies between results of different releases of Mykrobe and what we see in BAM files in IGV, which I will raise in a separate issue report.

davidjstudholme commented 1 year ago

In the meantime, if you are able to use the command-line version of Mykrobe this supports Staph if you install from my fork (waiting for #89 to be merged and then this will be in a new release).

Has this been actioned now? In other words, is there a recent release of Mykrobe that can handle Staph. aureus?

iqbal-lab commented 1 year ago

Oof. I'm sorry David, I think it was, but since then we've had some other stuff happen. Our automated setup for building the GUI had to be taken down, and we need to migrate it and re set it up. Our plan is to do this in the next few months, but right now we're quite diverted by covid analysis. I'm afraid on current plans we won't have a new GUI release until September. Let me check next week and see if i can accelerate that

davidjstudholme commented 1 year ago

Thanks for the prompt response, Zamin. Don't worry on my account; we can use Michael Hall's fork or the original Mykrobe PRedictor distributed as Supplementary Data in your Nature Biotechnology paper.