Using refgenie with iGenomes

If you're already using iGenomes, it's easy to configure refgenie to use your existing folder structure. iGenomes is project that provides sequences and annotation files for commonly analyzed organisms. Each iGenome is available as a compressed file that contains sequences and annotation files for a single genomic build of an organism.

Initialize a refgenie config file if you don't have one you want to use for your iGenomes assets:

export REFGENIE='genome_config.yaml'
refgenie init -c $REFGENIE

And then add individual assets you want refgenie to track with refgenie add:

refgenie add -g GENOME -a ASSET -p RELATIVE_PATH

So, for example,

wget ftp://igenome:[email protected]/Caenorhabditis_elegans/UCSC/ce10/Caenorhabditis_elegans_UCSC_ce10.tar.gz
tar -xf Caenorhabditis_elegans_UCSC_ce10.tar.gz
refgenie init -c igenome_config.yaml
refgenie add -c igenome_config.yaml -g ce10 --asset bowtie2_index --path Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index

Now we can seek any of those assets:

refgenie seek -c igenome_config.yaml -g ce10 --asset bowtie2_index

Or remove unwanted/faulty ones:

refgenie remove -g ce10 --asset bowtie2_index

This way you can configure refgenie to use your iGenomes assets, so you can wean yourself off of the iGenomes hard structure and transition to the refgenie-managed path system.