I am not wholly unfamiliar with the capabilities and costs involved in sequencing. While I have not (yet) worked on the Illumina platform I have worked/am currently working with SOLiD, ION, PacBio and 454 performing at least a sequence a week up to occasionally 2 sequences a day.

Yes, the costs of sequencing can be high. Start to finish a 454 run is ~$20,000, that is no small chunk of change. However, an ION run is an order of magnitude less. And OxNano is claiming to be $900 or less per run. This is why I laid it out the way I did; Deep sequence your reference genome (454, Illumina, SOLiD) as a baseline and subsequent sequences do not need to be as deep (fraction chips on 454, ION, PacBio). Also, I never constrained the hypothetical project to only performing a single sequence per morph either, I said rapid fire the morphs. The much reduced runtimes of the TGS systems would allow someone to potentially pull off an average of 3-4 sequences per day.

Additionally, I disagree that a single run is, necessarily, insufficient for acquiring the data you want. I grant that you would need to perform multiple sequence runs in a case where a SNP is responsible for the mutant phenotype. Obviously in a case like this you would have to to be able to confirm the SNP. But mutations are caused by more than just SNPs, there are in/dels, rearrangements, duplications... Mutations like these would be fairly obvious in a single sequence run. I do not think all of the 60 base mutations are going to be this easy to find but I do think a good number would be so you would not have to repeat sequence runs (n) times over for each and every mutation. And if someone was feeling really creative they could do comparative transcriptomes in addition to the genomes which could sign post loci.

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