gc_bias_plot

Plot bin coverage as a function of GC.

Plots the coverage of windows within each genome bin as a function of their GC content, using reads mapped to the sequences in a BAM file. The BAM file must be sorted and indexed (i.e. a .bai index file must be present; see coverage).

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

Arguments

usage: checkm gc_bias_plot [-h] [--image_type {eps,pdf,png,ps,svg}] [--dpi DPI]
                           [--font_size FONT_SIZE] [-x EXTENSION] [--width WIDTH]
                           [--height HEIGHT] [-w WINDOW_SIZE] [-r] [-a MIN_ALIGN]
                           [-e MAX_EDIT_DIST] [-t THREADS] [-q]
                           bin_input output_dir bam_file

Plot bin coverage as a function of GC.

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
  bam_file              BAM file to interrogate for coverage information

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: 3.5)
  -w, --window_size WINDOW_SIZE
                        window size used to calculate plot statistics (default: 5000)
  -r, --all_reads       use all reads to estimate coverage instead of just those in proper pairs
  -a, --min_align MIN_ALIGN
                        minimum alignment length as percentage of read length (default: 0.98)
  -e, --max_edit_dist MAX_EDIT_DIST
                        maximum edit distance as percentage of read length (default: 0.02)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output

Example: checkm gc_bias_plot ./bins ./plots example.bam

Example

checkm gc_bias_plot ./bins ./plots example.bam