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epitome

Pipeline for creating comprehensive viral reference sets.

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

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary

Keywords

data-wrangler genome-assembly reference-genomes viral-genomics
Last synced: 6 months ago · JSON representation ·

Repository

Pipeline for creating comprehensive viral reference sets.

Basic Info
  • Host: GitHub
  • Owner: DOH-JDJ0303
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 2.67 MB
Statistics
  • Stars: 10
  • Watchers: 1
  • Forks: 0
  • Open Issues: 4
  • Releases: 8
Topics
data-wrangler genome-assembly reference-genomes viral-genomics
Created almost 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

EPITOME: Enhanced Phylogenetic Inference Through Optimized Mapping Efficiency

EPITOME condenses a diverse set of DNA sequences into discrete, composite sequences that represent the overarching diversity of the dataset. In other words, EPITOME creates sequences that are the epitome of the dataset diversity. This is accomplished by clustering the input based on pairwise genetic distances and then selecting the most common nucleotide at each genomic position (ties selected at random). When the genetic distance is based on read mapping efficiency, EPITOME creates a set of reference genomes for consensus-based assembly pipelines, like VAPER.

See the wiki for more information.

Quick Start

Step 1. Create your samplesheet

[!NOTE] The example below creates a reference set for each taxon using data automatically downloaded from NCBI. It is also possible to supply your own sequence data with or without the NCBI data - learn more here.

samplesheet.csv: taxon,segmented,segmentSynonyms Hantavirus,TRUE,s|small;m|medium|middle;l|large Norovirus,FALSE,

Step 2. Run EPITOME

Run EPITOME using the command below. nextflow run DOH-JDJ0303/epitome \ -r main \ -profile docker \ --input samplesheet.csv \ --outdir results

Owner

  • Login: DOH-JDJ0303
  • Kind: user

Citation (CITATIONS.md) 

# nf-core/refmaker: 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: 7
  • Issues event: 3
  • Release event: 2
  • Watch event: 6
  • Delete event: 3
  • Issue comment event: 5
  • Member event: 1
  • Push event: 55
  • Gollum event: 50
  • Pull request event: 7
Last Year
  • Create event: 7
  • Issues event: 3
  • Release event: 2
  • Watch event: 6
  • Delete event: 3
  • Issue comment event: 5
  • Member event: 1
  • Push event: 55
  • Gollum event: 50
  • Pull request event: 7

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 3
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • DOH-JDJ0303 (3)
Pull Request Authors
  • DOH-JDJ0303 (10)
  • dependabot[bot] (1)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels
dependencies (1)

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/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi