Sophie's choice: Random mate-pairs or gel selection in Illumina?

[Marcela Uliano]

Hi guys!

I'm sequencing and assembling a de novo invertebrate genome of about 0,8Gb. I want to make a lane run of Illumina nextera mate-pairs, but I'm having some difficulty on selecting the size of the mate-pairs.

I saw that for de novo genomes is better if you have mate-pair-known sizes. So I was planning on doing 5kb and 10kb gel-size selection. However, the standard Illumina procedure is to make a random library of inserts ranging from 2kb to 15kb.

I was wondering how much bias it would insert for the de novo algoritm, lets say, allPaths, to assemble it? Does anyone of you have experience with that?

I don't know if I insist on trying to have the mate-pair with known insert size or if I just go for the random mate-pair library preparation (I have plenty of pair-ends already).

Any experinces you have, or papers to share, would help a lot! Thank you so much!

[svitlana]

Hello Marcela,

I need the same information for my assembly. Did you finally find something about it?

Thank you in advance