Please the TAIR9 genome to Galaxy next-gen tools for use with BowTie.
I made a "fasta" file you could use for this - it's here:
The genome version should be called:
A_thaliana_Jun_2009 or TAIR9
for best compatibility with Integrated Genome Browser (www.bioviz.org/igb).
Arabidopsis researchers (and many others!) use IGB to visualize tiling array results, annotations, EST alignments, Illumina short read alignments, and various other types of data.
The genome file is from the Arabidopsis Information Resource. If you need to contact them about this, just write to email@example.com.
Thank you and very best wishes!
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081