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2. Installation

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Laura Carroll edited this page Feb 23, 2022 · 4 revisions

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
  1. Activate your btyper3 environment by running the following command from your terminal:
conda activate btyper3
  1. Install BTyper3 by running the following command from your terminal:
conda install -c bioconda btyper3
  1. 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
  1. 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:

python3

Biopython v. 1.7.4 and up (for python3)

Pandas (for python3)

NumPy (for python3)

BLAST v. 2.9.0+ and up (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)

FastANI version 1.0 and up

  1. Add BLAST+ to your path, if necessary (to check if BLAST+ is in your path, try running makeblastdb -h and tblastn -h from your command line; you should get a help message for each command, with no error messages)

  2. Optional: Add fastANI to your path, if necessary (to check if fastANI is in your path, try running fastANI -h from your command line; you should get a help message, with no error messages). Note that this step is optional; if you want to perform species and/or subspecies and/or pseudo-gene flow unit assignment using BTyper3, you can just use the --fastani_path argument and supply the path to the fastANI executable (--fastani_path /path/to/fastANI)

  3. Install via pip:

pip install btyper3

Disclaimer: BTyper3 is pretty neat! However, no tool is perfect, and BTyper3 cannot definitively prove whether an isolate is pathogenic or not. As always, interpret your results with caution. We are not responsible for taxonomic misclassifications, misclassifications of an isolate's pathogenic potential or industrial utility, and/or misinterpretations (biological, statistical, or otherwise) of BTyper3 results.

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