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Open Source Science

https://github.com/alberdilab/squirrel_genomics

Code repository for the squirrel genomics project

https://github.com/alberdilab/squirrel_genomics

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Code repository for the squirrel genomics project

Basic Info
  • Host: GitHub
  • Owner: alberdilab
  • Default Branch: main
  • Size: 1.95 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 12 months ago · Last pushed 12 months ago
Metadata Files
Readme

README.md

Squirrel genomics

Code repository for the squirrel genomics project

1. Open screen session

Open a screen session to run the pipeline in the background. The session has the same name as the directory for the sake of simplicity.

sh screen -S 2025_squirrel_genomics

2. Prepare directory with pipeline

Clone the AlberdiLab genotyping pipeline repository to the server.

sh git clone https://github.com/alberdilab/genotyping mv genotyping 2025_squirrel_genomics cd 2025_squirrel_genomics

Download Snakemake wrappers to avoid connection issues.

sh git clone --depth 1 --branch v7.2.0 https://github.com/snakemake/snakemake-wrappers.git workflow/wrappers/v7.2.0

3. Fetch sequencing data

Download raw sequencing data from the EHI repository. This takes a while.

sh wget https://raw.githubusercontent.com/alberdilab/squirrel_genomics/refs/heads/main/reads.csv wget -P resources/reads -i reads.csv

4. Download reference genome

Download the red squirrel reference genome from the NCBI.

sh wget -P resources/reference https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/686/455/GCA_902686455.2_mSciVul1.2/GCA_902686455.2_mSciVul1.2_genomic.fna.gz

5. Launch pipeline

Launch Snakemake pipeline and wait until the final variant calling file is generated.

sh snakemake --workflow-profile profile/slurm

Owner

  • Name: alberdilab
  • Login: alberdilab
  • Kind: organization

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