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Old 07-06-2008, 02:06 PM   #1
mchaisso
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Default Paired-end Illumina data

Does any body have paired end illumina data they are willing to share for the purposes of testing euler-sr? I'd prefer bacterial genomes, and am willing to sign any required non-disclosure agreements.

Thanks,
-mark
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Old 07-06-2008, 02:34 PM   #2
ScottC
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How about the K12 genome from CLC. It's provided for evaluation of their Genomics Workbench. They have Illumina (E. coli K12), ABI (S. suis) and Roche (E. coli K12) data sets. Click the link below saying "Alternatively, you can download the raw data here".

http://www.clcbio.com/index.php?id=1290
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Old 07-06-2008, 02:46 PM   #3
mchaisso
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Quote:
Originally Posted by ScottC View Post
How about the K12 genome from CLC. It's provided for evaluation of their Genomics Workbench. They have Illumina (E. coli K12), ABI (S. suis) and Roche (E. coli K12) data sets. Click the link below saying "Alternatively, you can download the raw data here".

http://www.clcbio.com/index.php?id=1290
Thanks for the link... they are an interesting company.

I should mention that I'm looking for anything but K12.
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Old 07-06-2008, 09:29 PM   #4
cgb
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theres about 300GB of paired end illumina data at NCBI - all Human.
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Old 07-06-2008, 09:50 PM   #5
mchaisso
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... more clarification ...
ideally bacterial or small fungal genomes. I'm working on de novo assembly, and my code isn't mature enough to handle the complicated mammalian repeat structure.

Last edited by mchaisso; 07-06-2008 at 09:55 PM.
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Old 07-07-2008, 06:54 PM   #6
Torst
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The NCBI short read archive might have some.

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi

It certainly has some 454 FLX (paired) data, and some "Illumina GA" data for Bacteria, but unclear if it is paired.
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Old 07-17-2008, 12:12 AM   #7
lh3
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This is what Clive was talking about:

ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000271/

40X human resequencing. All PE reads. They have been there for a month or so. (Sorry, not for bacteria...)
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Old 07-17-2008, 11:52 AM   #8
EMeyer
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Mark,

I know its not what you were asking for in this post, but if a set of 454 reads (~600k raw reads) would be useful for testing Euler-SR, I'd be happy to share those with you in exchange for a quick explanation of the output from this program
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