Release to BRC

How to Create and Release GFF3 files to the BRCs

We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data.

• Creating the files

Choose a machine that is upto date, and create an empty directory. Run the command

nmpdr2gff NMPDR

This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set.

Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism):

• NMPDR
  • Campylobacter
    • Campylobacter.coli.RM2228.gff3
    • Campylobacter.jejuni.subsp.jejuni.84-25.gff3
    • ...
  • Listeria
    • Listeria.innocua.Clip11262.gff3
    • Listeria.monocytogenes.EGD-e.gff3
    • ...
  • Staphylococcus
    • Staphylococcus.aureus.RF122.gff3
    • Staphylococcus.aureus.subsp.aureus.MRSA252.gff3
    • ...
  • Streptococcus
    • Streptococcus.pneumoniae.R6.gff3
    • Streptococcus.pyogenes.MGAS10270.gff3
    • ...
  • Vibrio
    • Vibrio.cholerae.MO10.gff3
    • Vibrio.cholerae.O395.gff3
    • ...