GAIIx - maximum genome?

[vebaev]

What is the avarage maximum MB of the plant/animal genome that can be de novo sequenced with GAIIx? Is there a limit?

[simonandrews]

Theoretically there isn't a limit. If you want to run enough lanes you can sequence anything you could do with a HiSeq - it would just work out more expensive.

We've recently worked out costing for sequencing a ~400Mbp genome using a GAIIx. You basically need to use one whole flowcell for this whereas on a HiSeq you'd only need 3 lanes (and would actually get higher coverage from those, but the amount of data from the GA would be more than enough). In this case the costs on a HiSeq would be cheaper than the GA, but not ridiculously so. Once your genome gets much bigger than this I can't see the GA being economic.

If you're mostly going to be focussed on genome sequencing, even of smallish genomes then I'd be looking at a HiSeq rather than a GA. In our case the genome sequencing is an unusual run, so the GA works well for us still.

[vebaev]

We'll do mostly small RNAs and mRNA-seq, but we have one plan to seq a plant woth ~1000MB genome.

Just for info what was the overall total cost of consumables for your 400MB genome on GAIIx? and how many runs you did it with?


Thanks!

[simonandrews]

We'll do mostly small RNAs and mRNA-seq, but we have one plan to seq a plant woth ~1000MB genome.

If it's just a one off it would be worth finding out what it would cost to outsource this to a sequencing service. You could still do all of the library prep in house if you wanted and just get them to do the sequencing.

Just for info what was the overall total cost of consumables for your 400MB genome on GAIIx? and how many runs you did it with?

I don't have the break down to hand. The costs we had were full costings including staff time, instrument depreciation and all sorts of other stuff in addition to the cost of reagents.