ampligone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

https://github.com/rivm-bioinformatics/ampligone

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary

Keywords

amplicon-sequencing bioinformatics illumina nanopore ngs-analysis pcr python rivm

Last synced: 6 months ago · JSON representation ·

Repository

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

Basic Info

Host: GitHub
Owner: RIVM-bioinformatics
License: agpl-3.0
Language: Python
Default Branch: main
Homepage: https://rivm-bioinformatics.github.io/AmpliGone/
Size: 2.71 MB

Statistics

Stars: 20
Watchers: 1
Forks: 0
Open Issues: 1
Releases: 23

Topics

amplicon-sequencing bioinformatics illumina nanopore ngs-analysis pcr python rivm

Created almost 5 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog License Citation

README.md

GitHub release (latest by date including pre-releases) GitHub
GitHub deployments

AmpliGone

AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment.

In contrast to a lot of other primer-removal tools, AmpliGone does not actively look for primer sequences within the NGS reads. Instead, reads are trimmed based on primer sequence coordinates in relation to a given reference sequence. Additionally, AmpliGone is able to compensate for, and therefore properly clean, reads that start or end outside of a primer-region as this is a common occurrence in amplicon-based sequencing data.

AmpliGone is build and tested with Nanopore and Illumina data (fastq) in mind and supports 'end-to-end', 'end-to-mid' and 'fragmented' amplicons to be cleaned.
Please see this page to learn more about this terminology.

Installation instructions

AmpliGone can be installed easily with conda or pip. Installation through conda is recommended.

Installation with conda

bash conda install -c bioconda ampligone

Installation with pip

bash pip install AmpliGone

Please see the documentation for more information as well as extended installation instructions and usage instructions.

AmpliGone is freely available under the AGPLv3 license.

If you use AmpliGone in your work, please cite us as follows:

Zwagemaker, F., Hajji, K., Raaijmakers, G., Schmitz, D., Kroneman, A. AmpliGone [Computer software]. https://doi.org/10.5281/zenodo.7684307

Owner

Name: Infectieziekteonderzoek, Diagnostiek en laboratorium Surveillance-Bioinformatics (RIVM, The Netherlands)
Login: RIVM-bioinformatics
Kind: organization
Location: Netherlands

Website: https://www.rivm.nl/en/international
Repositories: 17
Profile: https://github.com/RIVM-bioinformatics

Citation (CITATION.cff)

cff-version: 1.2.0
title: "AmpliGone"
message: "If you use AmpliGone for your data analysis, then please cite it as below"
authors:
  - given-names: Florian
    family-names: Zwagemaker
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
    orcid: 'https://orcid.org/0000-0001-7788-0307'
  - given-names: Karim
    family-names: Hajji
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
    orcid: 'https://orcid.org/0009-0002-6384-3446'
  - given-names: Gino
    family-names: Raaijmakers
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
    orcid: 'https://orcid.org/0009-0003-3294-1999'
  - given-names: Dennis
    family-names: Schmitz
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
    orcid: 'https://orcid.org/0000-0002-6383-2643'
  - given-names: Annelies
    family-names: Kroneman
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
version: 2.0.1 #x-release-please-version
doi: 10.5281/zenodo.7684307
identifiers:
  - type: doi
    value: 10.5281/zenodo.7684307
    description: This is the collection of archived snapshots of all versions of AmpliGone
repository-code: 'https://github.com/RIVM-bioinformatics/AmpliGone'
url: >-
  https://rivm-bioinformatics.github.io/AmpliGone/latest/
abstract: >-
  AmpliGone is a tool in order to accurately remove primer
  sequences from NGS reads in an amplicon experiment
license: AGPL-3.0

GitHub Events

Total

Create event: 7
Issues event: 2
Release event: 2
Watch event: 5
Delete event: 2
Issue comment event: 21
Push event: 27
Pull request review event: 3
Pull request review comment event: 3
Pull request event: 17

Last Year

Create event: 7
Issues event: 2
Release event: 2
Watch event: 5
Delete event: 2
Issue comment event: 21
Push event: 27
Pull request review event: 3
Pull request review comment event: 3
Pull request event: 17

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 149
Total Committers: 7
Avg Commits per committer: 21.286
Development Distribution Score (DDS): 0.631

Top Committers

Name	Email	Commits
Florian Zwagemaker	f**n@n**m	55
Florian Zwagemaker	f**r@g**m	41
Karim Hajji	k**i@r**l	30
github-actions[bot]	4**]@u**m	14
ids-bioinformatics	8**s@u**m	4
Florian Zwagemaker	4**r@u**m	4
Karim Hajji	7**i@u**m	1

Committer Domains (Top 20 + Academic)

rivm.nl: 1 niqex.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 8
Total pull requests: 90
Average time to close issues: 3 months
Average time to close pull requests: 11 days
Total issue authors: 3
Total pull request authors: 5
Average comments per issue: 1.13
Average comments per pull request: 0.42
Merged pull requests: 87
Bot issues: 0
Bot pull requests: 38

Past Year

Issues: 2
Pull requests: 16
Average time to close issues: 6 months
Average time to close pull requests: 10 days
Issue authors: 1
Pull request authors: 4
Average comments per issue: 0.5
Average comments per pull request: 0.75
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 4

View more stats

Top Authors

Issue Authors

florianzwagemaker (6)
BertBog (1)
Thomieh73 (1)

Pull Request Authors

github-actions[bot] (38)
florianzwagemaker (35)
ids-bioinformatics (9)
raaijmag (8)
KHajji (3)

Top Labels

Issue Labels

enhancement (5) bug (2) good first issue (1)

Pull Request Labels

autorelease: tagged (20) enhancement (3) autorelease: pending (1)

Packages

Total packages: 1
Total downloads:
- pypi 34 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 11
Total maintainers: 3

pypi.org: ampligone

AmpliGone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon sequencing experiment

Documentation: https://ampligone.readthedocs.io/
License: agpl-3.0
Latest release: 2.0.1
published 11 months ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 34 Last month

Rankings

Dependent packages count: 10.1%

Stargazers count: 20.4%

Forks count: 29.8%

Average: 32.2%

Downloads: 33.5%

Dependent repos count: 67.2%

Maintainers (3)

IDS-bioinformatics florianzwagemaker KHajji

Last synced: 6 months ago

Dependencies

docs-requirements.txt pypi

mike *
mkdocs *
mkdocs-material *
mkdocs-material-extensions *

setup.py pypi

biopython >=1.79
mappy >=2.17
numpy >=1.20
pandas >=1.2.3
parmap >=1.5.2
pysam >=0.16
regex >=2021.11.10
tqdm >=4.59.0

.github/workflows/publish.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/release.yml actions

GoogleCloudPlatform/release-please-action v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
canastro/copy-file-action master composite

.github/workflows/sync.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite
tretuna/sync-branches 1.4.0 composite