We are trying to index the UMD 3.1.1 Bovine genome using the HISAT2 software.
The problem is that we need more than 200 Gbytes of memory for the hisat2-build script, and we were unable to get enough hardware resources in the Argentine scientific computing network. We assume more than 200Gb because of this note in the HISAT2 manual:
If you use --snp, --ss, and/or --exon, hisat2-build will need about 200GB RAM for the human genome size as index building involves a graph construction.
Do you know any facility, preferably free of charge, where we could run the indexer, provided that I already wrote a script which automates all the steps ?
To download and run the script, evaluate:
git clone https://github.com/hernanmd/hisat2_bovine.git ./make_bgumd31.sh