Is De-Bruijn graph only the best approach for assembling short reads from 2nd generation sequencing technologies?

Question

[saranpons3]

Hello All,

I would like to know that

"Is De-Bruijn graph only the best approach for assembling short reads from 2nd generation sequencing technologies?" or are there any other better approaches for assembling short reads from 2nd generation sequencing technologies?

what would be the maximum read length with which De-Bruijn graph approach will work best?

Please reply and thanks in advance.

[d-cameron]

Genome Assembly Review Papers has some good background reading on short read assembly.

[Brian Bushnell]

There's no maximum read length for De-Bruijn graph assembly. It becomes less efficient as error rates increase, which is why it is not suitable for PacBio or Nanopore reads.

Answer 1

[Medhat]

De-Bruijn graph used for assembly cause of its speed over overlap layout consensus OLC that means it is not the only way to assembly short reads, regarding length I read a paper about correcting long PacBio reads using de bruijn graph that means that the length could reach to 60,000 bp , what work best it depends cause in de bruijn graph you use k-mer which difference between organisms based on different factors

a nice table compare the different approaches could be found here http://www.nature.com/nrg/journal/v14/n3/box/nrg3367_BX2.html

another nice paper Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph