Where can I find public dataset of NGS?

xinwu · 09-01-2010, 01:35 AM

Hi all,
Where can I download public dataset of NGS? I only know one:

NCBI SRA(Short Reads Archive)

Data for whole genome resequencing is prefered.
Thanks.

krobison · 09-01-2010, 05:49 AM

Given that SRA has a huge number of datasets, what is it you can't find there?

I believe the European Nucleotide Archive freely exchanges with SRA, but with a time lag, so they are nearly identical in content.

Best way to query SRA I've found is via BioConductor module SRAdb -- it truly runs rings around the current web interfaces (where European archive is better than NCBI by a small notch), assuming you know SQL (which is easy enough to learn if you don't).

It also depends on what you are planning to do with the dataset; there are a limited number of actual assemblies available in BAM format which can be accessed using SAMtools via FTP/HTTP; see this prior thread for more on that.

xinwu · 09-02-2010, 06:11 PM

Hi Krobison,
Thanks a lot. We're planning to make a shorts reads assembly software review and comparison and look for a de facto standard data set as our benchmark. Although human genome is a well candidate, we prefer to find some plant genome. Thanks for your tips.

Joann · 09-08-2010, 01:11 PM

Hi Keith,

Can you suggest a good standard list of SRA's for general reference use and international benchmarking purposes? You know, a variety of samples--a plant, an animal, a microorganism or even an environmental sample. And details on where these data sets might be obtained by a user via the web.

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09-01-2010, 01:35 AM	#1
xinwu Member Location: Beijing Join Date: Jul 2010 Posts: 33	Where can I find public dataset of NGS? Hi all, Where can I download public dataset of NGS? I only know one: NCBI SRA(Short Reads Archive) Data for whole genome resequencing is prefered. Thanks. Last edited by xinwu; 09-01-2010 at 01:38 AM.

09-08-2010, 01:11 PM	#4
Joann Senior Member Location: Woodbridge CT Join Date: Oct 2008 Posts: 231	Any suggestions Hi Keith, Can you suggest a good standard list of SRA's for general reference use and international benchmarking purposes? You know, a variety of samples--a plant, an animal, a microorganism or even an environmental sample. And details on where these data sets might be obtained by a user via the web.

09-01-2010, 05:49 AM	#2
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	Given that SRA has a huge number of datasets, what is it you can't find there? I believe the European Nucleotide Archive freely exchanges with SRA, but with a time lag, so they are nearly identical in content. Best way to query SRA I've found is via BioConductor module SRAdb -- it truly runs rings around the current web interfaces (where European archive is better than NCBI by a small notch), assuming you know SQL (which is easy enough to learn if you don't). It also depends on what you are planning to do with the dataset; there are a limited number of actual assemblies available in BAM format which can be accessed using SAMtools via FTP/HTTP; see this prior thread for more on that.

09-02-2010, 06:11 PM	#3
xinwu Member Location: Beijing Join Date: Jul 2010 Posts: 33	Hi Krobison, Thanks a lot. We're planning to make a shorts reads assembly software review and comparison and look for a de facto standard data set as our benchmark. Although human genome is a well candidate, we prefer to find some plant genome. Thanks for your tips.