coverage

[neoanderson]

hi all,
is there a way to estimate the coverage we would get with 454 runs ?
i.e. if i have a 6mb prokaryotic genome of interest and would like to get data out of it on quarter of a 454 plate...how much coverage can I get?
is there a way to correlate genome size and coverage using any web based tools?

[nickloman]

It is pretty easy to do by hand.

454 Titanium generates 400-600 megabases per run (2 regions).

I.e. 200-300 megabases per region ("half-plate").

Or 100-150 megabases per quarter plate.

So simply divide your genome size by throughput, so 100/6 - 150/6 = 16.6x - 25x coverage for your genome on a quarter plate.

In reality there are also losses associated if using rubber gaskets to divide into 4, 8 or 16th plates. I'd figure on maybe 15% loss each time you divide past the default 2 region configuration (conservative figure).

[neoanderson]

thank you very much for this.
I really appreciate it.
Im new to 454 actually ...

[kmcarr]

The attached PDF is from the current Roche/454 Sequencing Method Manual. The table at the bottom right shows the expected number of reads/bases from the various region sizes obtainable using gaskets. Using a 4 region gasket each region is expected to yield 60-110 Mbp of sequence data or 10-18X coverage for your 6 Mbp bug.