Illumina provides a ftp site where you can download all the files you
need to use TopHat and Cufflinks: Bowtie index and gtf files are
present for about 20 species. For most species, we do covered
different data sources (mainly NCBI, Ensembl and UCSC) as well as
This resource is called iGenomes.
You can find all the links here
and more information about iGenomes here
The annotations are few months old but we will have a full update in 2
weeks that will also include BWA Index files.
9885 Towne Centre Drive
San Diego, CA 92121