Where can I find public dataset of NGS?

[xinwu]

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]

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]

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]

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.