Running TB-Profiler for MDU
Project description
tbtAMR
tbtAMR implements TB-profiler and custom logic developed at MDU to identify mutations linked to AMR mechanisms in M. tuberculosis and generate reports suitable for public health in Victoria. It may also be suitable for use in research settings.
tbtAMR is now accredited to ISO15189 standard by NATA for use in Victoria Australia.
tbtAMR installation
In order to install tbtAMR conda is strongly recommended - installation instructions can be found here.
git clone git@github.com:kristyhoran/tbtamr.git
cd tbtamr
conda env create -f environment.yml
conda activate tbtamr
pip3 install .
tbtamr setup
tbtamr check
tbtAMR DB
tbtAMR comes with a modified mutational database, defined by validation at MDU for the purposes of reporting mutations in a public health and clinical setting in Victoria.
This database was created using tb-profiler create_db (from MDU fork of pathogen-profiler)
The following files are required in order to generate a custom database
genome.fastathe reference for mutations in the databasegenome.fasta.faigenome.gffbarcode.bed- a
csvfile- header
Gene,Mutation,Drug,Confers,Interaction
- header
Creation can be done by navigating to a storage directory and running
conda activate tb-profile-env
tb-profiler create_db -p <db_prefix> -c <path_to_csv> --custom --db_name <name_of_db> --db_commit <some_unique_string> --db_author <name_of_author> --db_date <date_created>
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