GC bias visualization

Introduction

This plotting package is also integrated in a bam file reporting tool. Check out branch report if you are interested in it. This package allows you to visualize sequence bias in sequencing data. In order to do so, the reference sequence is split into k-mers. K-mer size can be controllable with the flag --window-size. For every k-kmer the GC content and the coverage is calculated. These tuples are then visualized with a 2dhistogram. This plot is interesting to investigate low coverage areas which is why there is cut off at a coverage of 20. Example output:
Here we see an example plot of Microbacterium saperdae which has a high average gc content. This plot shows the sequencing bias in Comamonas testosteroni. It shows nicely that areas with no coverage are sequence dependant.

Installation

This package requires samtools>=1.11 in your PATH.
The package can be installed using pip.

git clone https://github.com/nahanoo/gc_bias.git
cd gc_bias
pip install .

Usage

Labels of the graph are specified in a json file. Example labels.json:

{
    "title": "Agrobacterium tumefaciens in At34.1",
    "xlabel": "GC content per window",
    "ylabel": "coverage per window",
    "theme": "plotly_dark"
}

Help page called with `plot_gc_bias -h`:  
usage: plot_gc_bias [-h] [--window_size WINDOW_SIZE] [--plotting_only]
                    reference bam_file labels output_dir

Plot GC bias with 2d histograms. The GC content in percent is
calculated using a window size. For every window the according
coverage is calculated. GC content and coverage tuples are then
visualized using plotly. This package requires SAMtools in your path.

positional arguments:
  reference             path to reference sequence in fasta.
  bam_file              path to sorted BAM file.
  labels                json file labels for plots. see
                        https://github.com/nahanoo/gc_bias for example
                        file.
  output_dir            output direcotry.

optional arguments:
  -h, --help            show this help message and exit
  --window_size WINDOW_SIZE
                        window size used for GC content calculations
                        [default 150]
  --plotting_only       if added, only the plot will be regenerated.