SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Public repositories for NGS data greener Bioinformatics 1 05-02-2011 01:42 PM
public data sets muchomaas Bioinformatics 2 06-08-2010 02:48 AM
Public dataset availability genlyai Bioinformatics 0 08-12-2009 08:43 AM
Public understanding of genomics Oxford Nanopore General 6 06-18-2009 05:02 AM
Public Helicos Data zee Bioinformatics 2 08-11-2008 09:14 PM

Reply
 
Thread Tools
Old 09-01-2010, 01:35 AM   #1
xinwu
Member
 
Location: Beijing

Join Date: Jul 2010
Posts: 33
Default 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.
xinwu is offline   Reply With Quote
Old 09-01-2010, 05:49 AM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

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.
krobison is offline   Reply With Quote
Old 09-02-2010, 06:11 PM   #3
xinwu
Member
 
Location: Beijing

Join Date: Jul 2010
Posts: 33
Default

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.
xinwu is offline   Reply With Quote
Old 09-08-2010, 01:11 PM   #4
Joann
Senior Member
 
Location: Woodbridge CT

Join Date: Oct 2008
Posts: 231
Default 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.
Joann is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:09 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO