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Phylloxera edited this page Sep 3, 2024 · 10 revisions

Citation

The paper describing the GEA pipeline is here. If you use GEA in published research, cite the GitHub page: https://github.com/Phylloxera/GEA-dev including version and date accessed. It is good practice to cite the software wrapped by the GEA pipeline.

Steps to run GEA on example data:

  1. Download the container. E.g., curl -L -O https://github.com/Phylloxera/GEA-dev/releases/download/v0.0.3/geacont.tgz
  2. Extract the container to your $HOME/software directory. E.g., tar -xzvf geacont.tgz -C $HOME/software/
  3. Extract the bash script to $HOME/software. E.g., apptainer exec $HOME/software/geacont cp /usr/local/src/GEAbash $HOME/software/
  4. Make a folder for putting your test data. E.g., mkdir geatest && cd geatest
  5. Download some test data (a few libraries from Guragain et al., 2023). E.g., curl -L -O https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/433/975/GCF_029433975.1_ASM2943397v1/GCF_029433975.1_ASM2943397v1_genomic.fna.gz --next -L -O https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/434/035/GCF_029434035.1_ASM2943403v1/GCF_029434035.1_ASM2943403v1_genomic.fna.gz --next -L -O https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/434/335/GCF_029434335.1_ASM2943433v1/GCF_029434335.1_ASM2943433v1_genomic.fna.gz
  6. Extract the assemblies. E.g., gunzip * && cd ..
  7. Run the pipeline with default options. E.g., $HOME/software/GEAbash -i geatest

Changes v0 to v1

  1. v1 has an -I (input type) option, so on the latest release step 7. would be E.g., $HOME/software/GEAbash -i geatest -I contigs

Logging

The pipeline's progress is written to the console. This is fine for small assembly datasets. For larger or raw datasets, consider using redirection and/or backgrounding.

Databases

The GEA pipeline creates local copies of the databases that it uses to annotate genomes. These are placed in your $HOME/share folder.

Results

The principal output of GEA is the tab-delimited file, results/metadata.txt. Metadata.txt can be opened in Excel. The number of rows corresponds to the number of assemblies annotated and the number of columns is dataset dependent. The annotation quality is expected to improve as the database coverage improves over time.

Help

  • To get the GEAbash help message, run the program without any arguments. E.g., $HOME/software/GEAbash
  • To get the geacont help message, run apptainer run-help. E.g., apptainer run-help $HOME/software/geacont

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