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What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and highly contaminated by other DNA).

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It would help to have a little more info. Are you looking at a specific marker gene, or are you trying to assemble long contigs of the original animals' genomes from a metagenome? What sort of sequencing technology? The read length and error rate could be a big problem for some of them. –  gchadwick Aug 13 '13 at 11:40

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I agree with @gchadwick that more infor would help.

However, based on my understanding of what you are trying to do (SNP genotyping on several genes), I suggest. 1) Enrich your DNA with DNA from the organism you want 2) Enrich your DNA with DNA in the desired regions (if any).

Solution: Target enrichment. You are probably aware that companies such as agilent, nimblegen and illumina offer target enrichment kist for next generation sequencing. However, if your DNA is soooo bad, I suggest performing target selection with PCR.

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