Downloading Genomes
While gig-map can be used to align genes against a collection of genomes which
you have already collected, it can also be useful sometimes to download a set of
genomes from the NCBI database. Thankfully, the NCBI website provides a fantastic
interface for selecting a group of genomes which can then be downloaded by gig-map.
To use this feature, first visit the NCBI Genome Portal
and select the collection of genomes which you would like to download. Once you have
filtered down to the best set of genomes, click on the "Download" button (on
the top-right corner of the genome list) to save a file (often called prokaryotes.csv)
to your computer. This file can then be used as an input to the gig-map download utility
to save that group of genomes to your computer.
To download the set of genomes or genes which are found in each of the
NCBI accessions in the CSV, use the tools download_genes or download_genomes. The only argument for each of these tools is the CSV
containing the list of NCBI accessions. The output files will be downloaded
to your working directory within the sub-folder genomes/ or genes/.
-
genome_csv: A CSV file containing the list of genomes to download, as described above
-
genomes/: A folder containing the downloaded genomes -
genomes.annot.csv.gz: A table of annotations for all of the downloaded genomes
or
-
genes/: A folder containing the downloaded genes (one file per genome) -
genes.annot.csv.gz: A table of annotations for all of the genomes which were used to download genes
Other useful references may be: