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Old 03-30-2010, 07:14 AM   #29
MattB
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Location: Norway

Join Date: Aug 2008
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Does anyone have experience with different assemblers and how they handle polymorphims when constructing contigs? So far I have assemblies from Newbler and clc for this dataset and from ABySS and clc for an Illumina dataset but I'm not sure how to compare between the different assemblers really.
I think overall the de novo assemblers handle SNPs quite OK (at least from my experience with CLC; Abyss and SOAPdenovo). I think SOAPdenovo chooses one of the SNP alleles at random for the contig sequence (ie. consensus), but others may use the 'major' allele. Using CLC, I realigned my reads back to my de novo reference, and used the SNP detector ('find variants'). This actually allows you to replace the SNP allele in your reference with the 'major' SNP allele if it wasn't already there.

I can't really comment on how the de novo assemblers compare in terms of SNP handling performance, but those mentioned above have worked OK for me with 50:50 SNPs..

Matt
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