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phage_genome_size

Plotted bacteriophage genome sizes

https://github.com/nataquinones/phage_genome_size

Science Score: 54.0%

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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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    DOI references
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Plotted bacteriophage genome sizes

Basic Info
  • Host: GitHub
  • Owner: nataquinones
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 13 MB
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed 10 months ago
Metadata Files
Readme Citation

README.md

Bacteriophage genome sizes

Motivation

What even is a "big" phage? Or a "small" one? I wanted a figure to discuss this very question in a talk, but I couldnt find a plot I actually liked. The closest thing was this figure from Hyman and Abedon (2012), which is helpful, but over a decade old, the y-axis labels are mysteriously missing (?), and more importantly, theres been a major taxonomic overhaul since then. So, I figured it was time for a much-needed update.

Notebooks

The jupyter notebook that generates the main plot can be found here.

The previous version generating the updated 2012 plot can be found here.

Data

All the raw data can be found in data/. It was downloaded from NCBI Virus, selecting for complete nucleotide sequences.

Contributions and usage

I did minimal data curation, so there are likely to be errors and odd outliers, but overall the numbers should be reasonable. If you spot any major issues in the code or visualization, please let me know! You can write an issue or contribute with a PR.

If you use these figures or code, please cite it like:

Quinones-Olvera, N. Bacteriophage genome sizes https://github.com/nataquinones/phagegenomesize/

Owner

  • Name: Natalia Quinones-Olvera
  • Login: nataquinones
  • Kind: user
  • Location: MA, USA
  • Company: Harvard University

Systems Biology PhD student @baymlab | Mobile Genetic Elements, Phage, Antibiotic Resistance, CRISPR-Cas

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Bacteriophage genome sizes
message: >-
  If you use these figures, please cite it using the  
  metadata from this file.
type: software
authors:
  - given-names: Natalia
    family-names: Quinones-Olvera
    email: nquinones@g.harvard.edu
    name-particle: Natalia
    affiliation: 'Harvard Medical School, Boston, MA, USA'
    orcid: 'https://orcid.org/0000-0002-4612-6819'
repository-code: 'https://github.com/nataquinones/phage_genome_size/'

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