BTyper3

In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes

Overview

BTyper3 is a command-line tool for taxonomically classifying Bacillus cereus group genomes using a standardized nomenclature.

The program, as well as the associated databases, can be downloaded from https://github.com/lmc297/BTyper3.

Post issues at https://github.com/lmc297/BTyper3/issues.

For more information, check out the BTyper3 wiki at https://github.com/lmc297/BTyper3/wiki.

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Installation

For more information, check out the BTyper3 wiki

conda (recommended)

To create a conda environment named btyper3 and install BTyper3 and all of its dependencies:

1. Install conda, if necessary
2. Create a new environment named btyper3 by running the following command from your terminal:

   conda create -n btyper3

3. Activate your btyper3 environment by running the following command from your terminal:

   conda activate btyper3

4. Install BTyper3 by running the following command from your terminal:

   conda install bioconda::btyper3

5. You can now run btyper3! Run the following command from your terminal to view all btyper3 options, or check the BTyper3 wiki for details:

   btyper3 --help

6. When you’re done with BTyper3, you can deactivate the btyper3 environment by running the following:

   conda deactivate

pip

1. To run BTyper3, please download and install the following dependencies, if necessary:

   • Python 3
   • BLAST v2.9.0+ and up