RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper
An ultra fast universal RNA-seq aligner that can optionally perform gene-level quantification on the fly. Note that while very fast, this tool requires a considerable amount of memory. As an example, hg19 requires about 30GB. See http://gettinggeneticsdone.blogspot.com.au/2012/11/star-ultrafast-universal-rna-seq-aligner.html Most of this wrapper was originally written by Jeremy Goecks, with kibbitzing and automated dependency installation by Ross Lazarus.
- **Memory**: To run efficiently, RNA-STAR requires enough free memory to
hold the SA-indexed reference genome in RAM. For Human Genome hg19 this
index is about 27GB and running RNA-STAR requires approximately ~30GB of RAM.
For custom genomes, the rule of thumb is to multiply the size of the
reference FASTA file by 9 to estimate the required amount of RAM.