The Tophat2 entry screen does not list the reference genomes, however Bowtie2 does list them ( the ones I have in the bowtie2_indices.loc). The bowtie2_indices.loc states that this file works for both Bowtie2 and Tophat2.

David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services

Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone: 617-627-5319

Fax: 617-627-3667

http://it.tufts.edu