bowtie multi-thread / memory, and SSD vs spindle

[agbiotec]

Hello,

I was wondering if anyone knows any studies (papers conference / journal, blog, other) for bowtie or bowtie2 performance in multi-core (core i7 6x) systems, and how performance is affected with using SSDs vs spindle disks. Also how much memory ideally per core, when running multi-threaded alignment against human genome indexes.

I am looking to build a box for the lab, and trying to figure out 2 things : how much memory per core, and whether there is significant advantage with SSD drives (given that TB storage is required for our sequencing and SSD is expensive!).

Also any ideas the group might have if SSD offers 100x speedup for bowtie, how to combine with large spindle storage. I am basically looking for a tower box in the lab, and while I could get an external spindle disk array and keep the SSD in the box, I want to avoid staging data back and forth.

[GenoMax]

Configuration questions such as this are difficult to answer satisfactorily since we don't know the full details of what exactly you are trying to do (kinds of analyses you expect)/your budget for the hardware/local considerations (how much analysis you expect to do, data backup strategy etc).

That said, aligners do their work in memory so having an adequate amount available is a must (32G+ and upto what ever you can afford/your motherboard will accommodate). You are going to find that the general recommendation of putting your OS on SSD and rest of the data on spindle disks would still hold. Keep in mind that no matter how many cores you have, you only have PCI-E to keep those cores fed and there is a limit on how much data you can push through it, even in high-end desktop boards (unless you are buying server class MB).

If you can give us some additional information about the questions I have in paragraph 1 then you can get more specific answers.

[GenoMax]

For reference also posted at: https://www.biostars.org/p/165975/