Questions about Bowtie/Bowtie2 pre-built indexes

[navd]

I have a few questions about the pre-built index files on the bowtie and bowtie2 websites:

Is it necessary to update the index files for each update? Namely, do I need to redownload the index files if I am updating from bowtie 0.12.8 to 0.12.9? Also, would I need to redownload the index files if updating from bowtie2 2.05 to the most recent bowtie2?


Also, does the version of Bowtie2 index files influence TopHat functionality?


Lastly, I downloaded the newer index files, but the date created seems to be earlier than the date created of the index files I had downloaded for 2.05; I was wondering why the index files for the newer version of bowtie2 are older than the index files I downloaded from before (when I installed 2.05).

[simonandrews]

You don't normally need to re-index your genomes for an updated version of bowtie. Bowtie2 used a completely different index format than bowtie1 so that required a new set of indices but in general it's not been required. I seem to remember there have been some releases which mention improved performance if the genomes are re-indexed but these have been relatively rare.