The GEA pipeline

Now assembles long reads!

description

Characterization of E. coli and Salmonella genomes using High Performance Computers (HPCs) and Center for Genomic Epidemiology (CGE) developed command-line tools and local copies of the CGE databases.

dependencies

• apptainer

quick start

• curl -L -O https://github.com/Phylloxera/GEA-dev/releases/latest/download/geacont.tgz
  

• tar -xzvf geacont.tgz
  

• apptainer run-help geacont
  

support

manual