Data

Tools

Indexes

Applications

Experiments

Open Source Science

vaper

Viral (meta)-genome assembly pipeline.

https://github.com/doh-jdj0303/vaper

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary

Keywords

bioinformatics genome-assembly public-health viral-genomics viral-metagenomics
Last synced: 6 months ago · JSON representation ·

Repository

Viral (meta)-genome assembly pipeline.

Basic Info
  • Host: GitHub
  • Owner: DOH-JDJ0303
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 156 MB
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 0
  • Open Issues: 4
  • Releases: 2
Topics
bioinformatics genome-assembly public-health viral-genomics viral-metagenomics
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

VAPER: Viral Assembly from Probe-based EnRichment

Key Features

VAPER is a viral (meta-)assembly pipeline that can:

🧬 Assemble genomes from complex samples, supporting multiple assemblies per sample (e.g., co-infections)
🧬 Automatically detect and select reference genomes
🧬 Predict the taxonomy of each assembly, with an optional viral metagenomic summary
🧬 Export reads associated with each assembly for downstream use

While VAPER was originally designed for hybrid capture data (e.g., Illumina VSP or Twist CVRP), it has also been used with shotgun metagenomic and tile-amplicon data. It comes stock with comprehensive reference sets for multiple taxa, including influenza A, SARS-CoV-2, and Monkeypox (full list). Keep on reading to learn more!

Pipeline Overview

VAPER Flowchart

More Information:

See the docs for more information.

Acknowledgements

VAPER would not be possible without the following people: - Holly Halstead (WA PHL) - Pauline Trinh (WA MEP) - Allison Black (WA MEP) - Stephanie Lunn (WA MEP) - Kristen Waterman (WA PHL) - Brandi Torrevillas (WSU)

VAPER was originally written by Jared Johnson for the Washington State Department of Health.

Owner

  • Login: DOH-JDJ0303
  • Kind: user

Citation (CITATIONS.md) 

# nf-core/waphlviral: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 8
  • Release event: 1
  • Issues event: 7
  • Watch event: 12
  • Delete event: 4
  • Member event: 2
  • Issue comment event: 1
  • Push event: 62
  • Pull request event: 10
  • Gollum event: 117
Last Year
  • Create event: 8
  • Release event: 1
  • Issues event: 7
  • Watch event: 12
  • Delete event: 4
  • Member event: 2
  • Issue comment event: 1
  • Push event: 62
  • Pull request event: 10
  • Gollum event: 117

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 5
  • Average time to close issues: about 8 hours
  • Average time to close pull requests: less than a minute
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 5
  • Average time to close issues: about 8 hours
  • Average time to close pull requests: less than a minute
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • DOH-JDJ0303 (3)
  • aswarren (2)
  • Vikash84 (1)
  • bktorrevillas (1)
Pull Request Authors
  • DOH-JDJ0303 (12)
Top Labels
Issue Labels
enhancement (5) bug (2)
Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/release-announcments.yml actions
  • actions/setup-python v4 composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action v0.0.2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/shovill/meta.yml cpan
pyproject.toml pypi
modules/nf-core/samtools/fastq/meta.yml cpan
modules/nf-core/seqtk/sample/meta.yml cpan
modules/nf-core/seqtk/subseq/meta.yml cpan
modules/nf-core/sourmash/gather/meta.yml cpan
modules/nf-core/sourmash/sketch/meta.yml cpan
modules/nf-core/krona/ktimporttext/meta.yml cpan
modules/nf-core/fastp/environment.yml conda
  • fastp 0.23.4.*
modules/nf-core/krona/ktimporttext/environment.yml conda
  • krona 2.8.1.*
modules/nf-core/seqtk/sample/environment.yml conda
  • seqtk 1.3.*
modules/nf-core/seqtk/subseq/environment.yml conda
  • seqtk 1.3.*
modules/nf-core/shovill/environment.yml conda
  • shovill 1.1.0.*
modules/nf-core/samtools/fastq/environment.yml pypi
modules/nf-core/sourmash/gather/environment.yml pypi
modules/nf-core/sourmash/sketch/environment.yml pypi