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Old 12-02-2012, 09:12 AM   #1
mht
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Default building consensus with multiple samples

Hi,

I have 4 samples with Illumina reads which I would like to build a consensus out of. The 4 samples are of the same species and there is a reference for it. I am looking into using Velvet Columbus, but I was wondering, is there a problem with pooling my reads together and proceeding with one assembly?

My aim is to call SNPs using this consensus.

Much thanks.
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Old 12-02-2012, 10:05 AM   #2
Apexy
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Going by an educated guess, you should pool them together if all are from the same library.
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Old 12-02-2012, 02:22 PM   #3
mht
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Yes, they're all Illumina reads. I was guessing it would be alright too if they're the same species, I have two parents and two progeny. I was just wondering if the presence of SNVs will affect the de novo assembly process.
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consensus sequence, reference guided assembly, velvet

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