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Old 09-18-2013, 10:20 AM   #1
Junior Member
Location: Tarragona

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Default is it possible to analyze NGS data without access to a server????

Hi everyone,

Currently I am not affiliated to any institution so I do not have access to any server, but I have access to some 454-NGS data which I would like to analyze to get my hands a bit on this field, as I am completely new in this.

The initial objective is to look for markers, microsats, but I thought that I could also try to do some assembling of the runs.

Can any of you give some reccomendations on computer characteristics that I should try to minimum have?? Like RAM, CPU, processor, ...

I am aware that if I finally run the analysis on a laptop or stationary computer (without access to server) it might take ages. Alternatively, does anyone know if a particular person can hire server space? and how much would that cost??

I'll be greatly thankful to any suggestions received
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Old 09-19-2013, 08:06 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

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While I do not use it myself, several packages (including Galaxy) run on the Amazon cloud. I suggest searching this forum for AWS or Amazon.
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Old 09-19-2013, 11:56 AM   #3
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Location: Eugene, OR

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Galaxy also has a public server. It can be slow for your particular analysis to move through the queue, but it should have the tools you need.
Providing nextRAD genotyping and PacBio sequencing services.
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Old 09-19-2013, 12:00 PM   #4
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How many data do you have? What analysis do you want to do?
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Old 09-19-2013, 12:33 PM   #5
Location: SF Bay Area

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Until you're dealing with multiple runs worth of data, you're fine on a 'regular' machine, supposing it has a good amount (16+gb) of ram. There are only a few things that won't run on such a machine overnight. If you're just trying to get some hands-on experience 'doing' the analysis, you don't need to be using a massive stack of data, and if you don't like how long your process is taking, you can always just take a subset of it.

The processing of data doesn't change much (or really at all, most of the time) on the user side when you scale it up. The analysis and results are affected by the changes, however.
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Old 09-19-2013, 12:36 PM   #6
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454 data is small compared to Illumina data. You should be able to analyze it on a desktop computer.
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Old 09-19-2013, 02:36 PM   #7
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I concur with the last couple of posts - there is little that you can't do with a desktop/laptop computer. Even assembly does not take that much memory if you use e g Minia.
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Old 09-19-2013, 06:10 PM   #8
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For microsatellite searching I can highly recommend the QDD algorithm, it doesn't use much in the way of resources and screens out potential multi-copy loci.
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Old 09-22-2013, 01:10 PM   #9
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Thanks I'll certainly have a look on this
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computer, ngs analysis, server

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