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Published 20 hours ago • verified publisher icon ngs-fzb

MTBseq Update?

Open peflanag opened this issue 2 years ago • 8 comments

Hi,

this is more a question than an issue. I am just wondering will there be an update of MTBseq anytime soon with the revised WHO mutation catalogue.

Cheers,

P

peflanag avatar Feb 01 '23 15:02 peflanag

Hi, actually yes! We are running some last tests and it will be available hopefully in the next days then!

cutpatel avatar Feb 02 '23 13:02 cutpatel

Awesome, cheers!

peflanag avatar Feb 02 '23 14:02 peflanag

It is great to hear that MTBseq has WHO mutation catalogue. Have you already updated the version of MTBseq ?

ryobon-dev avatar Mar 29 '23 01:03 ryobon-dev

Sry it took a bit longer, but the updated database is now online and included in the newest release v1.1.0.

cutpatel avatar Apr 05 '23 08:04 cutpatel

Thanks that's great. I'm trying to install into a new condo env to validated it in our laboratory but using conda install -c bioconda mtbseq doesn't seem to work. It's been hanging now for 4 hours.

Any ideas? I tried mamba install -c bioconda mtbseq but that just installed v1.04

peflanag avatar Apr 05 '23 12:04 peflanag

I think it will take some time until conda also updates.

To get the new predictions right now you can just copy this file: https://github.com/ngs-fzb/MTBseq_source/blob/master/var/res/MTB_Resistance_Mediating.txt And then exchange it manually in your conda installation in the /var/res/ directory.

cutpatel avatar Apr 05 '23 14:04 cutpatel

Cheers!

peflanag avatar Apr 13 '23 12:04 peflanag

I also meant to ask, will the update have the capabilities for --thread to increase the speed??

Cheers!

peflanag avatar Apr 13 '23 14:04 peflanag