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viroconstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

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

Science Score: 67.0%

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
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords

analysis bioinformatics consensus-sequences ngs-analysis public-health python rivm snakemake snakemake-workflow virology viruses
Last synced: 6 months ago · JSON representation ·

Repository

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

Basic Info
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 2
  • Open Issues: 6
  • Releases: 35
Topics
analysis bioinformatics consensus-sequences ngs-analysis public-health python rivm snakemake snakemake-workflow virology viruses
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

ViroConstrictor

install with bioconda DOI

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

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences from your data based on a given reference genome.

ViroConstrictor performs high speed data quality control, data cleanup and high accuracy removal of primer-sequences from NGS reads. As well as alignment of reads and generation of a consensus sequence using the TrueConsense consensus-caller which accounts for sequencing errors and alignment artefacts.

ViroConstrictor is able to run both on a standalone (linux) computer, as well as High-Performance Computing (HPC) infrastructures.

ViroConstrictor is compatible with Nanopore, Illumina, and IONTorrent data (fastq).

Please see the documentation for more information.

ViroConstrictor is available under the AGPLv3 licence

If you use ViroConstrictor in your work, please cite:

Zwagemaker, F., Hajji, K., Schmitz, D., Kroneman, A., & The RIVM-IDS Bioinformatics team. ViroConstrictor [Computer software]. https://doi.org/10.5281/zenodo.7688035

Owner

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

Citation (CITATION.cff) 

cff-version: 1.2.0
title: "ViroConstrictor"
message: >-
  If you use ViroConstrictor for your data analysis, then please cite it as:
  Zwagemaker, F., Hajji, K., Schmitz, D., Kroneman, A., & The RIVM-IDS Bioinformatics team. ViroConstrictor [Computer software]. https://doi.org/10.5281/zenodo.7688035
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: Dennis
    family-names: Schmitz
  - given-names: Annelies
    family-names: Kroneman
    affiliation: >-
      National Institute for Public Health and the
      Environment (RIVM)
  - name: "The RIVM-IDS Bioinformatics team"
version: 1.5.5 #x-release-please-version
doi: 10.5281/zenodo.7688035
identifiers:
  - type: doi
    value: 10.5281/zenodo.7688035
    description: This is the collection of archived snapshots of all versions of ViroConstrictor
repository-code: 'https://github.com/RIVM-bioinformatics/ViroConstrictor'
url: >-
  https://rivm-bioinformatics.github.io/ViroConstrictor/latest/
abstract: >-
  ViroConstrictor is a pipeline designed to process raw
  FastQ data from viral amplicon-based sequencing and
  generate biologically correct consensus sequences of a
  given viral genome
license: AGPL-3.0

GitHub Events

Total
  • Create event: 17
  • Release event: 5
  • Issues event: 4
  • Watch event: 2
  • Issue comment event: 41
  • Push event: 59
  • Pull request review comment event: 8
  • Pull request review event: 7
  • Pull request event: 39
Last Year
  • Create event: 17
  • Release event: 5
  • Issues event: 4
  • Watch event: 2
  • Issue comment event: 41
  • Push event: 59
  • Pull request review comment event: 8
  • Pull request review event: 7
  • Pull request event: 39

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 32
  • Average time to close issues: 5 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.69
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 4
  • Pull requests: 23
  • Average time to close issues: 5 days
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 4
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.65
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 6
View more stats
Top Authors
Issue Authors
  • florianzwagemaker (2)
  • raaijmag (1)
  • Jrb96 (1)
Pull Request Authors
  • github-actions[bot] (9)
  • florianzwagemaker (9)
  • ids-bioinformatics (8)
  • raaijmag (6)
Top Labels
Issue Labels
bug (2) enhancement (1)
Pull Request Labels
autorelease: pending (7)

Dependencies

docs-requirements.txt pypi
  • mike *
  • mkdocs *
  • mkdocs-material *
  • mkdocs-material-extensions *
setup.py pypi
  • biopython ==1.79
  • drmaa ==0.7.9
  • fpdf2 ==2.5.1
  • openpyxl ==3.0.9
  • pandas ==1.4.2
  • pyyaml ==6.0
  • urllib3 >=1.26
.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
.github/workflows/build_and_test.yml actions
  • actions/checkout v3 composite
  • actions/download-artifact v4 composite
  • actions/upload-artifact v4 composite
  • eWaterCycle/setup-apptainer v2 composite
  • mamba-org/setup-micromamba v1 composite
.github/workflows/publish_containers.yaml actions
  • actions/checkout v3 composite
  • dawidd6/action-download-artifact v8 composite
  • docker/login-action v3 composite
  • mamba-org/setup-micromamba v1 composite