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Old 02-01-2010, 06:21 PM   #1
Dave S.
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Default Dave - interested in trial data sets and high-throughput sequencing tutorials

Hi all:

I'm interested in learning how to analyze NGS data sets from the latest devices but have no access to the actual machines at my workplace. What are the best open sources of raw data to analyze?

I'd like to get up to speed on the essential NGS software and practice a bit with it. I am fluent in a couple programming languages (R, Perl, Java, C#, Python) but am not a "real" CS programmer (biologist by training).
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Old 02-02-2010, 05:57 AM   #2
krobison
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Anyone who says they are fluent in 5 computer languages should quite saying they are not a "real" programmer!

The NCBI Short Reads Archive & European Short Reads Archive are good sources for datasets. Many of the programs will run on a typical laptop or desktop, though for really big datasets you will run into challenges.

Bowtie is a good first program to try.

There are several reviews floating around on second generation sequencing data analysis; one of the Nature magazines (Biotech? Methods?) had a special section recently. Or, just take one of the recent publications from the Literature Watch section here & read it end-to-end including the methods & try to digest that.
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Old 02-02-2010, 07:39 AM   #3
drio
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Quote:
Originally Posted by Dave S. View Post
Hi all:

I'm interested in learning how to analyze NGS data sets from the latest devices but have no access to the actual machines at my workplace. What are the best open sources of raw data to analyze?

I'd like to get up to speed on the essential NGS software and practice a bit with it. I am fluent in a couple programming languages (R, Perl, Java, C#, Python) but am not a "real" CS programmer (biologist by training).
Bfast comes with a tool to generate synthetic reads (bfast/butil/bgeneratereads).

The software can introduce indels, SNPs, errors, etc...

bwa and maq have something similar too.

Figure out what is the current throughput from the different sequencers and generate data to "play" with it.

If you need to get closer to the sequencer, that is going to be more complicate. Start by downloading the manuals from your sequencer of choice and get the big picture of how the data flow happens.
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Old 02-02-2010, 07:52 AM   #4
Calico
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I am interested in this as well but I do not find most reviews and papers I have read helpful as for learning. Does anyone know any tutorial that really explains the procedures in detail?
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Old 02-02-2010, 11:04 AM   #5
Dave S.
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Default Thanks

Thanks for the info drio and krobinson.

Perhaps I'll see if the DNALinux people are interested in adding some of the NGS tools to the VM image and if so, I could build some of them in.

Ha, thanks for the "real programmer" comment. I tend to think of people who can write a video card driver in assembly as "real" programmers, but I guess that is the minority of even CS grads.
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