The usage and help documentation of dnadiff_dist_matrix.py can be seen by running pyhton dnadiff_dist_matrix -h:

usage: - [-h] [--min_coverage MIN_COVERAGE] [--fasta_names FASTA_NAMES]
         [--plot_image_extension PLOT_IMAGE_EXTENSION] [--skip_dnadiff]
         [--skip_matrix] [--skip_plot] [--cluster-threshold CLUSTER_THRESHOLD]
         output_folder fasta_files [fasta_files ...]

Output distance matrix between fasta files using dnadiff from MUMmer. Generates
dnadiff output files in folders:



where fastaname for each fasta file can be supplied as an option to the script.
Otherwise they are just counted from 0 to len(fastafiles)

The distance between each bin is computed using the 1-to-1 alignments of the
report files (not M-to-M):

1 - AvgIdentity if min(AlignedBases) >= min_coverage. Otherwise distance is 1.
Or 0 to itself.

Resulting matrix is printed to stdout and to output_folder/dist_matrix.tsv. The
rows and columns of the matrix follow the order of the supplied fasta files. The
names given to each fasta file are also outputted to the file

A hierarchical clustering of the distance using euclidean average linkage
clustering is plotted. This can be deactivated by using --skip_plot. The
resulting heatmap is in output_folder/hclust_heatmap.pdf or
output_folder/hclust_dendrogram.pdf and the resulting clustering is presented
in output_folder/clustering.tsv. The image extension can be changed.

positional arguments:
  output_folder         Output folder
  fasta_files           fasta files to compare pairwise using MUMmer's dnadiff

optional arguments:
  -h, --help            show this help message and exit
  --min_coverage MIN_COVERAGE
                        Minimum coverage of bin in percentage to calculate
                        distance otherwise distance is 1. Default is 50.
  --fasta_names FASTA_NAMES
                        File with names for fasta file, one line each. Could
                        be sample names, bin names, genome names, whatever you
                        want. The names are used when storing the MUMmer
                        dnadiff results as in
                        output_folder/fastaname1_vs_fastaname2/. The names are
                        also used for the plots.
  --plot_image_extension PLOT_IMAGE_EXTENSION
                        Type of image to plotted e.g. pdf, png, svg.
  --skip_dnadiff        Skips running MUMmer and uses output_folder as given
                        input to calculate the distance matrix. Expects
                        dnadiff output as
  --skip_matrix         Skips Calculating the distance matrix.
  --skip_plot           Skips plotting the distance matrix. By default the
                        distance matrix is clustered hierarchically using
                        euclidean average linkage clustering. This step
                        requires seaborn and scipy.
  --cluster-threshold CLUSTER_THRESHOLD
                        The maximum within cluster distance allowed.


An example of how to run dnadiff_dist_matrix on the test data:

cd CONCOCT/scripts
python dnadiff_dist_matrix.py test_dnadiff_out tests/test_data/bins/sample*.fa

This results in the following output files in the folder test_dnadiff_out/:

  • dist_matrix.stv The distance matrix
  • fasta_names.tsv The names given to each bin (or fasta file)
  • clustering.tsv This file will give a cluster assignment for each bin (or fasta file)
  • hcust_dendrogram.pdf Dendrogram of the clustering (click for example)
  • hcust_heatmap.pdf Heatmap of the clustering (click for example)

Then there is also for each pairwise dnadiff alignment the following output files in a subfolder fastaname1_vs_fastaname2/:


See MUMmer’s own manual for an explanation of each file with dnadiff --help.