Key concepts

• Organism: biological entity, e.g. a microbial strain
• Genome: one sample of a particular organism. Multiple genomes can be associated with one organism, e.g. if a particular strain has been sequenced multiple times
• The representative genome: the best available genome of an organism

Documentation

• Folder structure and metadata
• Annotations
• Orthologs and Orthofinder
• Pathway maps

A shortcut: opengenomebrowser-tools

The library opengenomebrowser-tools makes loading genome-associated files into the folder structure really simple.

For example, it only takes two commands to annotate an assembly using prokka and import it into the folder structure:

export FOLDER_STRUCTURE=/path/to/folder_structure

init_folder_structure  # requires the opengenomebrowser-tools python library

prokka \
  --strain STRAIN \ 
  --locustag STRAIN.1 \
  --genus Mycoplasma --species genitalium \
  --out /prokka/out/dir \
  assembly.fasta

import_genome --import_dir=/prokka/out/dir  # requires the opengenomebrowser-tools python library

Nevertheless, it is a good idea to have some idea of how OpenGenomeBrowser works.