Command line usage

Installing this package creates a command mtbdiff that you can call in a terminal. Before running this tool you will need to have prepared full or partial genomes in fasta files, one per sample. If you have done sequencing and have the raw read data you should first create de novo assemblies using SPAdes or another assembler for bacterial genomes.

Options

  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        Input folder
  -o OUTPATH, --output=OUTPATH
                        Output folder
  -r REF, --ref=REF     Reference fasta file (not required)
  -t, --test            Do tests

Example

If you have a set of assemblies/full genomes in fasta files, place them in one folder. This is the input. You can also select an output folder for the results. You don't need to provide a reference genome unless you want to use your own. The default reference is the MTB H37Rv genome.

Then call the command using:

mtbdiff -i my_genomes -o results

Results

In the results folder you'll find a directory for each sample with the nucdiff results. There will also be the following files:

• ref_struct.csv: contains a table of all the changes relative to the reference for all samples.
• summary.csv: summary of the changes common to all samples and the frequency of each.