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Old 10-26-2009, 04:22 PM   #1
balamudiam
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Default Helicos sequencing machine data & format required

Hello all,

I am a graduate student working on sequence assembler for assembling short reads produced by latest technology sequencing machines like Helicos. The existing assembler, we developed works with ABI Solid data. We would like to enhance it and get it working on other sequence machine data too.

I had a touch time trying to find the Helicos genome data format and data. Can someone point me to the data and the format.

Regards
Bala Mudiam
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Old 10-26-2009, 07:57 PM   #2
ECO
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Have you tried http://open.helicosbio.com/mwiki/index.php/Main_Page or http://www.ncbi.nlm.nih.gov/sites/sra ?
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Old 10-27-2009, 06:55 AM   #3
krobison
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Specifically, http://www.ncbi.nlm.nih.gov/sites/en...43&report=full is the data for the Stephen Quake genome sequencing.
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Old 10-27-2009, 07:55 AM   #4
Chipper
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Quote:
Originally Posted by krobison View Post
Specifically, http://www.ncbi.nlm.nih.gov/sites/en...43&report=full is the data for the Stephen Quake genome sequencing.
Do you know how to access this dataset? I have tried to download it through the ftp but was not able to find the files, and the download link above does not work.
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Old 10-27-2009, 09:28 PM   #5
krobison
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Nuts! This seems to be a recurring issue with the Short Read Archive -- the records are created but for some reason the data doesn't show up right away. Try contacting NCBI -- they are very helpful and can probably tell you what the holdup is.
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