Will a SSD improve Bowtie or Tophat performance?

biznatch · 11-16-2011, 09:27 PM

My computer has dual hard drives, one SSD and one traditional spinning HDD. Will keeping any of the files used in Bowtie or Tophat alignments on the SSD instead of the HDD speed up the process? Eg. The index files, input sequence reads, output files, or (in the case of Tophat) temp files. Other specs are i7-2720QM (2.2-3.3GHz), 16GB RAM. I'm thinking the bottleneck is probably the CPU since the threads almost always run at nearly 100% but thought I would ask.

simonandrews · 11-17-2011, 12:47 AM

An SSD won't help for this type of analysis. Bowtie maps the genome indices into memory, so once it's loaded the only activity from the disk should be writing out results files.

As you've seen the limitation is CPU. Bowtie allows you to spread your CPU load over many cores using the -p parameter and performance increases linearly with number of CPUs up to at least 8 cores in our tests. Tophat can also take advantage of this, but some parts of the code (calculating putative splice sites) are not multi-threaded, so will only use a single CPU.

biznatch · 11-17-2011, 08:54 AM

Thanks for the reply, I figured as much. I use 6-8 cores depending on if I need the computer for anything else while the alignments are running.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.	rebrendi	Bioinformatics	11	06-22-2016 10:55 AM
High performance computing & Tophat & Cufflinks	paolo.kunder	Bioinformatics	1	01-24-2012 09:02 AM
Tophat help: how to maximize CPU performance	lewewoo	Bioinformatics	3	10-19-2011 06:09 PM
How to Improve Newbler Assembly	shuang	Bioinformatics	2	09-13-2011 10:45 PM
Bowtie -p/--threads parameter for increased performance	thinkRNA	Bioinformatics	4	03-05-2010 11:31 AM

11-16-2011, 09:27 PM	#1
biznatch Senior Member Location: Canada Join Date: Nov 2010 Posts: 124	Will a SSD improve Bowtie or Tophat performance? My computer has dual hard drives, one SSD and one traditional spinning HDD. Will keeping any of the files used in Bowtie or Tophat alignments on the SSD instead of the HDD speed up the process? Eg. The index files, input sequence reads, output files, or (in the case of Tophat) temp files. Other specs are i7-2720QM (2.2-3.3GHz), 16GB RAM. I'm thinking the bottleneck is probably the CPU since the threads almost always run at nearly 100% but thought I would ask. Last edited by biznatch; 11-16-2011 at 09:33 PM.

11-17-2011, 12:47 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	An SSD won't help for this type of analysis. Bowtie maps the genome indices into memory, so once it's loaded the only activity from the disk should be writing out results files. As you've seen the limitation is CPU. Bowtie allows you to spread your CPU load over many cores using the -p parameter and performance increases linearly with number of CPUs up to at least 8 cores in our tests. Tophat can also take advantage of this, but some parts of the code (calculating putative splice sites) are not multi-threaded, so will only use a single CPU.

11-17-2011, 08:54 AM	#3
biznatch Senior Member Location: Canada Join Date: Nov 2010 Posts: 124	Thanks for the reply, I figured as much. I use 6-8 cores depending on if I need the computer for anything else while the alignments are running.