pip install amplicov

conda install -c bioconda amplicon_coverage_plot 

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

cd amplicon_coverage_plot
python setup.py install

amplicov -h

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

cd tests
./runTest.sh