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Old 03-30-2010, 06:40 AM   #28
natstreet
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Location: Sweden

Join Date: Nov 2009
Posts: 83
Default SNPs and de novo assembly

I'm working in a similar dataset that I've inherited - 454 transcriptome runs from 30 pooled individuals. I've been wondering how assembler handle major frequency SNPs. Would contigs be split in two at sites of a SNP that's present in a roughly 50:50 ratio in your reads or would one or the other variant be selected as a representative base at that position?

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.
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