454 sequencing data coverage

[Salmon]

Dear All,

I am currently working on 454 sequencing data. The average length of reads is ~200bp, and coverage is ~8-10X.

Does anybody tell me how the data coverage is? Is it ok or not?
Because when I do annotation, I found many many single nucleotide changes (mutation/insertion/deletion).

Thank you.

[sklages]

de-novo or refguided?

We usually work with ~30x coverage when dealing with both denovo and refguided assemblies (FLX), Though you might need a bit less for refguided. This is for bacterial genome size projects (1-8Mb) here.

Sven

[hlu]

We usually do 20x de novo assembly. This works for either FLX or Titanium.

Sounds that you are still doing FLX.

454 Titanium paired end data improved a lot compared to FLX paired end. Now I would think perferrably, 10x shot gun, and 10x paired end.

Recently I did a de novo assembly on a , 454 machine can run 2 pads in same runs. 1 pad for shot gun, another pad for paired end data in same run. The fungi assembly worked well for us.

[kmcarr]

454 Titanium paired end data improved a lot over compared to FLX paired end.

hlu,

I don't think the Titanium paired end kits are available yet. Are you doing a home brew paired end with Titanium?

[hlu]

hlu,

I don't think the Titanium paired end kits are available yet. Are you doing a home brew paired end with Titanium?

I am using early access 454 Titanium pairs end kits.

There are not out there yet public. I heard from 454 sales that they will be out possibly within a month. So it will be there soon.