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Old 09-05-2013, 07:08 AM   #1
skymj
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Location: columbus

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Default Estimation time on de novo assembly

Hi folks:
I am trying to do a de novo assembly. The pair read length is around 100bp, we have around 600 million reads. The estimated size of the genome is 3Gb. Can anyone give me some suggestions on which specific de novo assembly software best fit to this scale and is there an estimation equation to calculate how long it could take?
Many thanks!
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Old 09-05-2013, 02:48 PM   #2
jimmybee
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Quote:
Originally Posted by skymj View Post
Hi folks:
I am trying to do a de novo assembly. The pair read length is around 100bp, we have around 600 million reads. The estimated size of the genome is 3Gb. Can anyone give me some suggestions on which specific de novo assembly software best fit to this scale and is there an estimation equation to calculate how long it could take?
Many thanks!
It all depends on the genome (complexity, heterozygousity) and the computer resources you have available. Theres no 'one assembler fits this data' you're going to have to have a go at a few and compare. A good starting point would be to have a look at how they assembled the closest relative

Have a look at the Assemblethon papers for tips and reviews about the specifics of each assembler
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Old 09-05-2013, 05:14 PM   #3
lh3
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That is 20X over 3GB. You should be able to assemble that in a couple of days to a couple of weeks, depending on the assemblers.
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