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Laura Carroll edited this page Feb 23, 2022 · 1 revision

BTyper3 Tutorial #1: Characterizing a B. cereus isolate using its draft genome

  1. First, let's download our isolate's draft genome from NCBI by clicking the follwoing link:

https://www.ncbi.nlm.nih.gov/Traces/wgs/JHQN01

If not already selected, click the "Download" tab. Click on the link for the FASTA file to download the contigs in fasta format: JHQN01.1.fsa_nt.gz. This should download the file into your "Downloads" directory.

  1. If you haven't done so already, open your terminal. For Mac users, type command-space to open your search bar, type terminal in your search bar, and press Enter. For Ubuntu users, type Ctrl-Alt-t (assuming you haven't changed your default shortcuts).

  2. From the command line in your terminal, move to your "Downloads directory" by typing the following, and then hitting Enter:

cd ~/Downloads
  1. Now that we're in our Downloads directory, let's unzip our contigs file by typing the following command, and hitting Enter:
gunzip JHQN01.1.fsa_nt.gz
  1. Let's create an output directory in which we can store our BTyper3 results. That way, once we're done with this tutorial, we can easily delete everything. To create a directory called "btyper3_tutorial_1" in our Downloads directory, type the following command and hit Enter:
mkdir ~/Downloads/btyper3_tutorial_1
  1. Now, let's run BTyper3 on our genome, directly from our Downloads directory, by typing the following command into our terminal, and pressing Enter:
btyper3 -i ~/Downloads/JHQN01.1.fsa_nt -o ~/Downloads/btyper3_tutorial_1

Here are the options we selected, explained:

  • -i ~/Downloads/JHQN01.1.fsa_nt We're directing BTyper3 to our input file (JHQN01.1.fsa_nt)

  • -o ~/Downloads/btyper3_tutorial_1 We're telling BTyper3 where to store the output files it produces (our directory, btyper3_tutorial_1)

  1. Once the program is finished running, we can take a look at our final results file to get detailed results about our isolate. Open the "JHQN01.1_final_results.txt" file in any text editor, either by searching for it or opening it in your "~/Downloads/btyper3_tutorial_1/btyper3_final_results" directory.

  2. Now that we've opened the final results file for our isolate, we can see all taxonomic classifications for our isolate in the column "final_taxon_names". According to BTyper3, our genome's full taxonomic classification is B. mosaicus biovar Anthracis. This can also be written as B. Anthracis, meaning that our genome possesses anthrax toxin-encoding genes! We can see that all three toxin genes, cya, lef, and pagA, were detected in our genome (column "anthrax_toxin(genes)"). No cereulide synthetase genes were detected (column name "cereulide(genes)").

Sure enough, this genome is actually that of strain BcFL2013, an isolate previously classified as "anthrax-causing B. cereus which was isolated from a patient with an anthrax-like skin lesion in Florida (Gee, et al., 2014, Genome Announcements).

  1. If you want to delete the results from this tutorial, just go to your Downloads folder and delete the "btyper3_tutorial_1" directory there.

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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