How to load genomes into CoGe

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There are two general programs to run:

  • 'fasta_genome_loader.pl:
    • Loads in fasta sequences into CoGe
  • annotation loader:
    • usually some version of gff_annotation_loader.pl or some other program for loading text based gene models and annotations


UAGC Example

The UAGC produces many genomic sequences. This is to help them streamline their procedure for loading genomes into CoGe

  1. Get 454AllContigs.fna
    1. This is the usual contig-level genome assembly from the 454 genome sequencing pipeline
  2. run fasta_genome_loader.pl
~/projects/CoGeX/scripts/fasta_genome_loader.pl \
-org_name "Acidovorax sp. strain JS42 substrain KSJ2" \
-org_desc "Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Acidovorax;" \
-source_name "University of Arizona Genetics Core" \
-source_link "http://uagc.arl.arizona.edu/" \
-ds_version .1 \
-nt KSJ2_454AllContigs.fna \
-dsg_restricted 1
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