which gap filler do you recommend?

Question

[Mostafa]

Does anyone have useful experience or know some paper in comparing different gap fillers like Sealer, FGAP, GapCloser (part of SOAPdenovo), and etc?

thanks

[WouterDeCoster]

Hi shahhosseini.94,

It is unclear which data you have available. Please elaborate to explain your question better.

Cheers,
Wouter

[Mostafa]

We have a draft genome which its size is about 1.52Gb. its generated from some libraries of paired-end and mate pair reads. Actually, its assembled from 3 paired-end and 3 mate pair library with a coverage between 16x and 70x. in addition to the data which are assembled to our draft genome, we have a 10X linked reads library which has not been inserted in our draft genome.

don't hesitate to ask if you have some other questions?

thanks.

[h.mon]

Shouldn't you start by assembling a new genome with all data available?

[Mostafa]

it's a good approach which we are following in parallel by using abyss assembler for assembling the whole data, 10X added to them. but using gap fillers can be useful in any case. am I right?

[h.mon]

Yes, probably useful in any case (my personal experience with gap filling has been disappointing, just marginal improvements at best). But you don't want to test every iteration possible, it will be just a waste of time and energy. So to me it makes sense to get the assembly with all data available, then gap-fill / polish it.

On the other hand, I totally get trying several approaches: I am curious and like to do this myself. But most often than not, the simpler, more obvious approach ends up being the better one.

Answer 1

[k.kathirvel93]

I would recommend Genome finishing module from CLCGenomicsworkbench. Go with trail version if you cannot afford the software.