Miseq de novo assembly : Ambigous base pairs (NNs) in the contigs

[ndeshpan]

Hi,

I am using MiSeq paired-end reads (250X) coverage ..quality trimmed ..for de novo assembly using abyss ..

In the assembly (non-scaffolded file) I am getting streches of "NNNs" which I guess could represent

Ambigous reads

I want to check if :

Error correction softwares can be used to avoid this? Saying this I have read that most of the assemblers already have this step incorporated in them..

Can anyone put more light on their experience assembing "MiSeq" data and getting the above problems?

regards,

Nandan

[fahmida]

I think it is helpful for others to comment with a bit more information, for example species, genome size etc. The following link seems to discuss something along your problem:

https://groups.google.com/forum/#!msg/abyss-users/8E5609CSrUY/1NkZIDO6rx0J

[ndeshpan]

Thanks

Thanks, your link was very useful

cheers