README.md

amplicon_coverage_plot

The script will generate an interactive barplot given amplicon info in bed6/bedpe format and coverage information in cov/bam file.

Dependencies

Programming/Scripting languages

• Python >=v3.8
  • The pipeline has been tested in v3.8.10

Python packages

• numpy >=1.15.1
• plotly >=4.7.1
• pysam >= 0.15.4

Third party softwares/packages

• samtools >=1.9 - process bam file

Installation

Install by pip

pip install amplicov

Install by conda

conda install -c bioconda amplicon_coverage_plot 

Install from source

Clone the amplicon_coverage_plot repository.

git clone https://github.com/chienchi/amplicon_coverage_plot

Then change directory to amplicon_coverage_plot and install.

cd amplicon_coverage_plot
python setup.py install

If the installation was succesful, you should be able to type amplicov -h and get a help message on how to use the tool.

amplicov -h

Usage

usage: amplicov [-h] (--bed [FILE] | --bedpe [FILE])
                (--bam [FILE] | --cov [FILE]) [-o [PATH]] [-p [STR]] [--pp]
                [--mincov [INT]] [--version]

Script to parse amplicon region coverage and generate barplot in html

optional arguments:
  -h, --help            show this help message and exit
  --pp                  process proper paired only reads from bam file
                        (illumina)
  --count_primer        count overlapped primer region to unqiue coverage
  --mincov [INT]        minimum coverage to count as ambiguous N site
                        [default:10]
  -r [STR], --refID [STR]
                        reference accession (bed file first field)
  --depth_lines DEPTH_LINES [DEPTH_LINES ...]
                        Add option to display lines at these depths (provide depths as a list of integers) [default:5 10 20 50]
  --gff [FILE]          gff file for data hover info annotation
  --version             show program's version number and exit

Amplicon Input (required, mutually exclusive):
  --bed [FILE]          amplicon bed file (bed6 format)
  --bedpe [FILE]        amplicon bedpe file

Coverage Input (required, mutually exclusive):
  --bam [FILE]          sorted bam file (ex: samtools sort input.bam -o
                        sorted.bam)
  --cov [FILE]          coverage file [position coverage]

Output:
  -o [PATH], --outdir [PATH]
                        output directory
  -p [STR], --prefix [STR]
                        output prefix

Test

cd tests
./runTest.sh

Outputs

-- prefix_amplicon_coverage.txt

ID	Whole_Amplicon	Unique	Whole_Amplicon_Ns(cov<10)	Unique_Amplicon_Ns(cov<10)
nCoV-2019_1	217.74	53.00	0.00	0.00
nCoV-2019_2	1552.83	1235.50	0.00	0.00
nCoV-2019_3	3164.22	2831.73	0.00	0.00
nCoV-2019_4	2005.16	1658.00	0.00	0.00
etc...

Table Header Definition in the amplicon_coverage.txt

• Whole_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Whole Amplicon region

• Unique_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Unique region

-- prefix_amplicon_coverage.html

color black for < 5x and blue for <20x