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Old 12-30-2014, 02:40 AM   #1
gilst
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Smile Hardware requirements for various tools

Hi All

New to sequencing.
I am planning on running BWA, GATK and possibly VarScan.
Does anyone know what are the hardware requirements for running these programs in terms of CPU and RAM?

Many thanks
Gil
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Old 12-30-2014, 03:04 AM   #2
GenoMax
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Expected genome size? Number of samples/users?
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Old 12-30-2014, 03:08 AM   #3
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I just want to run 1 human exome.
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Old 12-30-2014, 03:10 AM   #4
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2 files with a size of 2.4 GB each for paired end sequencing
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Old 12-30-2014, 03:13 AM   #5
GenoMax
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For a single sample any PC/Mac/Linux machine of recent vintage (core i5, i7, xeon) would likely do. You would want to have at least 8GB (16G preferable) RAM.

If you have access to an institutional compute cluster/server then consider using that resource rather than a local computer.
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Old 12-30-2014, 03:17 AM   #6
gilst
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I was actually asked to try to use cloud computing. They charge by the hardware that you need. That is why I was asking for the program requirements.
Will 16GB RAM suffice or would I need 30?
I was told that BAM files which are an intermediate step of GATK are 15GB so I assumed I would need more for the program to run properly.
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Old 12-30-2014, 03:24 AM   #7
GenoMax
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See this recent paper to give you an idea of needs in terms of cloud computing: http://www.biomedcentral.com/1756-0500/7/314 You should start with a large instance if you are going to use GATK.
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Old 12-30-2014, 03:53 AM   #8
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They do not give the information I require but rather the configuration they used (in Amazon) but thanks anyway.

Last edited by gilst; 12-30-2014 at 03:55 AM.
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Old 12-30-2014, 04:12 AM   #9
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Here are some specific recommendation about the GATK part from Broad: https://www.broadinstitute.org/gatk/...rticle?id=1975

Heng Li (author of BWA) recommended this for BWA: http://seqanswers.com/forums/showthread.php?p=102458 and more recently: http://sourceforge.net/p/bio-bwa/mai...sage/32268544/

You will ultimate need to decide how long you are willing to wait for the analysis to complete.

Paper had used m2.xlarge instance (you can find the hardware specs here: http://aws.amazon.com/ec2/previous-generation/, you can map the hardware specs to current generation here: http://aws.amazon.com/ec2/instance-types/) on Amazon. If you prefer using something else then translate the hardware requirements accordingly.

Last edited by GenoMax; 12-30-2014 at 04:18 AM.
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