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everest_meta

https://github.com/agudeloromero/everest_meta

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
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    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: agudeloromero
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 79.1 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

EVEREST-meta (pipEline for Viral assEmbly and chaRactEriSaTion for METAgenomics)

This version, meta, is adapted for pair-end and single-end reads. DOI

EVEREST is a snakemake pipeline for virus discovery, its main purpose is to characterise phage genomes isolates but can be also used for all the virome.

Running EVEREST:

  1. Clone EVEREST repository. (base)$ git clone --recursive https://github.com/agudeloromero/EVEREST_meta.git

  2. Create everest environment Creating conda environment for Snakemake and EVEREST from the file everest.yml, provided in this repository. (base)$ conda create env -n everest -f everest.yml (base)$ conda activate everest (everest)$

  3. Databases for EVEREST are available here: https://zenodo.org/records/8404860.

How to run EVEREST:

  • Edit conf/config.yml file to point the input, output and databases directories.
  • The databases include the human genome as a reference to get rid off those reads. However, this link can be changed by an alternative genome. Example of how to download other genomes of interest can be seen here https://github.com/agudeloromero/Reference_Genomes. $ conda activate everest (everest)$ snakemake --use-conda -j 2 --keep-going Input directory should contain the .fastq.gz files to analyse ( -j option have to be set depending on number of available cores). Files are expected to be named as "nameR1" and "nameR2" plus extension. In case you need to rename then, please see this example (https://github.com/agudeloromero/renamefastqfiles).
  1. Summary files can be explored with everest shiny app: https://agudeloromero.shinyapps.io/everest/

Owner

  • Name: Patricia
  • Login: agudeloromero
  • Kind: user
  • Location: Perth, Australia
  • Company: Telethon Kids Institute

Mother and computational biologist. Studying host-microbiome interaction. Having fun coding :)

Citation (CITATION.cff) 

#https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Agudelo-Romero"
  given-names: "Patricia"
  orcid: "https://orcid.org/0000-0002-3703-4111"
- family-names: "Conradie"
  given-names: "Talya"
  orcid: "https://orcid.org/0009-0007-6380-5737"
- family-names: "Kicic"
  given-names: "Anthony"
  orcid: "https://orcid.org/0000-0002-0008-9733"
- family-names: "Caparros-Martin"
  given-names: "Jose"
  orcid: "https://orcid.org/0009-0007-6380-5737"
- family-names: "Stick"
  given-names: "Stephen"
  orcid: "https://orcid.org/0000-0002-5386-8482"

title: "EVEREST_meta"
version: v0.1.0
doi: 10.5281/zenodo.10487446
date-released: 2024-01-11
url: "https://github.com/agudeloromero/everest_meta"

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