Long Reads Assembly

[mido1951]

hello,

Do you have any references for assembling long reads?
I searched but I wanted to know if there are other algorithms assemblies of long reads.

thank you friends

[sBeier]

The first question is, what do you mean with long reads? 600 bp Illumina MiSeq? Sanger sequences? PacBio reads? And the second is, what are the algorithms you already found? Otherwise we cannot tell what algorithm would be another possibility.

[mido1951]

thank you for your reply.
I search the algorithms assembling of long reads with all technologies of sequencing (Sanger, PacBio ...). I am looking for references (articles, theses, ...).
thank you for your help.

[sBeier]

I guess the algorithm you already found is Overlap Layout Consensus. The first algorithms for assembly were improvements of basic sequence alignment, since the first sanger reads could be aligned manually and the real need for assembling computationally started with shotgun sequencing and the higher amount of data and shorter reads this produced. The need to assemble long reads is now coming back, but so far mainly existing tools have been adapted to work with long reads. Overlap Layout Consensus has been originally used for Sanger reads, so it is the obvious one to mention. String graph assembly is also working well for long reads, because it uses the connectivity information of a read without splitting it up like a de-bruijn based assembler would. I am not aware of an algorithm that is exclusively meant to be used with long reads, but I hope I could give you some topics to look into.

[mido1951]

other responses?

[pacbio]

Check out this recent webinar for a range of assembly tools/strategies for long reads: Optimizing Eukaryotic De Novo Genome Assembly w Long-Read Sequencing by Mike Schatz (CSHL), James Gurtowski (CSHL), and Serge Koren (NBACC)

http://aa314.gondor.co/webinar/optimizing-eukaryotic-de-novo-genome-assembly-with-long-read-sequencing/