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Old 03-04-2013, 05:10 PM   #1
Junior Member
Location: California

Join Date: Mar 2013
Posts: 3
Default Questions about Bowtie/Bowtie2 pre-built indexes

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).
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Old 03-05-2013, 12:22 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

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.
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bowtie, bowtie2, index files, tophat

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