nx_plot

Create Nx-plots.

Produces a plot indicating the Nx value of a genome bin for all values of x. This provides a more comprehensive view of the quality of an assembly than simply considering N50.

A plot is written for each bin to <output_dir>/<bin id>.nx_plot.<image_type>.

Arguments

usage: checkm nx_plot [-h] [--image_type {eps,pdf,png,ps,svg}] [--dpi DPI] [--font_size FONT_SIZE]
                      [-x EXTENSION] [--width WIDTH] [--height HEIGHT] [-s STEP_SIZE] [-q]
                      bin_input output_dir

Create Nx-plots.

positional arguments:
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_dir            directory to hold plots

options:
  -h, --help            show this help message and exit
  --image_type {eps,pdf,png,ps,svg}
                        desired image type (default: png)
  --dpi DPI             desired DPI of output image (default: 600)
  --font_size FONT_SIZE
                        Desired font size (default: 8)
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  --width WIDTH         width of output image (default: 6.5)
  --height HEIGHT       height of output image (default: 6.5)
  -s, --step_size STEP_SIZE
                        x step size for calculating Nx (default: 0.05)
  -q, --quiet           suppress console output

Example: checkm nx_plot ./bins ./plots

Example

checkm nx_plot ./bins ./plots