{"id":25007152,"url":"https://github.com/chienchi/amplicon_coverage_plot","last_synced_at":"2025-04-23T14:20:46.448Z","repository":{"id":49568041,"uuid":"270555241","full_name":"chienchi/amplicon_coverage_plot","owner":"chienchi","description":" interactive barplot for amplicon sequencing","archived":false,"fork":false,"pushed_at":"2024-12-05T21:13:26.000Z","size":6388,"stargazers_count":13,"open_issues_count":3,"forks_count":5,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-30T00:24:51.460Z","etag":null,"topics":["amplicon","coverage","genome"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chienchi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-06-08T06:25:31.000Z","updated_at":"2024-12-05T21:13:30.000Z","dependencies_parsed_at":"2024-12-04T16:27:35.130Z","dependency_job_id":"90333b7f-3f69-4aa9-aefd-99ada9ca7516","html_url":"https://github.com/chienchi/amplicon_coverage_plot","commit_stats":{"total_commits":77,"total_committers":5,"mean_commits":15.4,"dds":0.6493506493506493,"last_synced_commit":"b99e0de7d7ee6620aedfb3131c6af153b1dd07e0"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chienchi%2Famplicon_coverage_plot","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chienchi%2Famplicon_coverage_plot/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chienchi%2Famplicon_coverage_plot/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chienchi%2Famplicon_coverage_plot/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chienchi","download_url":"https://codeload.github.com/chienchi/amplicon_coverage_plot/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250447982,"owners_count":21432166,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["amplicon","coverage","genome"],"created_at":"2025-02-05T01:53:28.233Z","updated_at":"2025-04-23T14:20:46.423Z","avatar_url":"https://github.com/chienchi.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# amplicon_coverage_plot\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14285656.svg)](https://doi.org/10.5281/zenodo.14285656)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/amplicon_coverage_plot/badges/version.svg)](https://anaconda.org/bioconda/amplicon_coverage_plot)\n[![Build Status](https://travis-ci.org/chienchi/amplicon_coverage_plot.svg?branch=master)](https://travis-ci.org/chienchi/amplicon_coverage_plot)\n[![codecov](https://codecov.io/gh/chienchi/amplicon_coverage_plot/branch/master/graph/badge.svg)](https://codecov.io/gh/chienchi/amplicon_coverage_plot)\n[![PyPI version](https://badge.fury.io/py/amplicov.svg)](https://badge.fury.io/py/amplicov)\n\nThe script will generate an [interactive barplot](https://chienchi.github.io/amplicon_coverage_plot/index.html) given amplicon info in [bed6/bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html) format and coverage information in cov/bam file.\n\n## Dependencies\n\n### Programming/Scripting languages\n- [Python \u003e=v3.8](https://www.python.org/)\n    - The pipeline has been tested in v3.8.10\n\n### Python packages\n- [numpy \u003e=1.15.1](http://www.numpy.org/) \n- [plotly \u003e=4.7.1](https://plotly.com/python/)\n- [pysam \u003e= 0.15.4](https://github.com/pysam-developers/pysam)\n\n### Third party softwares/packages\n- [samtools \u003e=1.9](http://www.htslib.org) - process bam file\n\n## Installation\n\n### Install by pip\n\n```\npip install amplicov\n```\n\n### Install by conda\n\n```\nconda install -c bioconda amplicon_coverage_plot \n```\n\n### Install from source\nClone the `amplicon_coverage_plot` repository.\n\n```\ngit clone https://github.com/chienchi/amplicon_coverage_plot\n```\n\nThen change directory to `amplicon_coverage_plot` and install.\n\n```\ncd amplicon_coverage_plot\npython setup.py install\n```\n\nIf the installation was succesful, you should be able to type `amplicov -h` and get a help message on how to use the tool.\n\n```\namplicov -h\n```\n\n\n## Usage\n```\nusage: amplicov [-h] (--bed [FILE] | --bedpe [FILE])\n                (--bam [FILE] | --cov [FILE]) [-o [PATH]] [-p [STR]] [--pp]\n                [--mincov [INT]] [--version]\n\nScript to parse amplicon region coverage and generate barplot in html\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --pp                  process proper paired only reads from bam file\n                        (illumina)\n  --count_primer        count overlapped primer region to unqiue coverage\n  --mincov [INT]        minimum coverage to count as ambiguous N site\n                        [default:10]\n  -r [STR], --refID [STR]\n                        reference accession (bed file first field)\n  --depth_lines DEPTH_LINES [DEPTH_LINES ...]\n                        Add option to display lines at these depths (provide depths as a list of integers) [default:5 10 20 50]\n  --gff [FILE]          gff file for data hover info annotation\n  --version             show program's version number and exit\n\nAmplicon Input (required, mutually exclusive):\n  --bed [FILE]          amplicon bed file (bed6 format)\n  --bedpe [FILE]        amplicon bedpe file\n\nCoverage Input (required, mutually exclusive):\n  --bam [FILE]          sorted bam file (ex: samtools sort input.bam -o\n                        sorted.bam)\n  --cov [FILE]          coverage file [position coverage]\n\nOutput:\n  -o [PATH], --outdir [PATH]\n                        output directory\n  -p [STR], --prefix [STR]\n                        output prefix\n```\n\n## Test\n\n```\ncd tests\n./runTest.sh\n```\n\n## Outputs \n\n-- prefix_amplicon_coverage.txt\n\n| ID          | Whole_Amplicon | Unique  | Whole_Amplicon_Ns(cov\u003c10) | Unique_Amplicon_Ns(cov\u003c10) |\n|-------------|----------------|---------|---------------------------|----------------------------|\n| nCoV-2019_1 | 217.74         | 53.00   | 0.00                      | 0.00                       |\n| nCoV-2019_2 | 1552.83        | 1235.50 | 0.00                      | 0.00                       |\n| nCoV-2019_3 | 3164.22        | 2831.73 | 0.00                      | 0.00                       |\n| nCoV-2019_4 | 2005.16        | 1658.00 | 0.00                      | 0.00                       |\n| etc...      |                |         |                           |                            |\n\n#### Table Header Definition in the amplicon_coverage.txt \n\n\u003cimg width=\"465\" alt=\"Screen Shot 2020-06-15 at 3 29 53 PM\" src=\"https://user-images.githubusercontent.com/737589/84708117-1fc2e480-af1d-11ea-8411-35210a8dd6fa.png\"\u003e\n\n* Whole_Amplicon_Ns(cov\u003c10): The number of aligned position with coverage \u003c 10 or (--mincov) in the Whole Amplicon region\n\n* Unique_Amplicon_Ns(cov\u003c10): The number of aligned position with coverage \u003c 10 or (--mincov) in the Unique region\n\n-- prefix_amplicon_coverage.html\n\n```color black for \u003c 5x and blue for \u003c20x```\n\n\u003ca href=\"https://chienchi.github.io/amplicon_coverage_plot/index.html\"\u003e![html](https://user-images.githubusercontent.com/737589/105805303-f2ccba80-5f5e-11eb-8338-63bd51bd426d.png)\u003c/a\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchienchi%2Famplicon_coverage_plot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchienchi%2Famplicon_coverage_plot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchienchi%2Famplicon_coverage_plot/lists"}