Should I run Gap close in assembly ?

Question

[Picasa]

Hi,

I'm not sure to understand what is the step "gap close" after getting scaffolds.

For instance, with SOAPdenovo or Platanus can make this after a scaffolding step.

I tried to perform it but my N50 get down dramatically, while my N% get down too.

After scaffolding: N50: 3616, %N: 30

After Gapclose: N50: 2217, %N: 2

1) So what is Gap closing ? I thought it was the removal of N bases but it looks that I still got it after that.

2) Should I run it ?? or I can stop after scaffolding step.

Answer 1

[Medhat]

In general gap clossing using SOAPdenovo uses De Bruijn graphs to create a local assembly and seek to fill the gaps with the resulting contigs. A drawback of these strategies is that no prior knowledge of the estimated gap size is taken into account.

so N's count should drop down by this step but if there is no coverage for some N's it will be still in your assembly, also now the size of your genome increases as a result the N50 will decrease.

On the other have you can use GapFiller If you have mate pairs

where paired reads are (re)used. In brief, our GapFiller method seeks to find read pairs of which one member matches within a sequence region and the second member falls (partially) within the gap. The latter reads are then used to close the gap through sequence (k-mer) overlap. Gaps are entirely closed only if the size of the sequence insertion corresponds closely to the estimated gap size after scaffolding, which is based on the alignment of paired reads to the contigs

you could also find this helpful

Illumina Assembly Gap Closure

Good luck :)