Hi all! First post here, maybe some of you can shed some light on this:
We are working on a denovo sequencing and assembly project, of an eukaryotic genome of ~120 Mbp. So far we have sequenced a couple of fragment libraries with 454 titanium. We now want to sequence some paired-end libraries, but the sequencing facility has problems with getting the titanium 20kbp inserts (and the 8Kbp) to work. 3Kbp inserts seem to work fine, so the question is:
Is there a big difference between 20Kbp and 3Kbp inserts when it comes to the assembly (L50, N50 etc.)?
I have been asking around, and the answer I get is that "of course 20Kbp is better". What I am interested in is how much better it would be (if its worth to wait for x months). These things are difficult to estimate, but if maybe somebody has some experience from similar projects...?
thanks
/Jakub
We are working on a denovo sequencing and assembly project, of an eukaryotic genome of ~120 Mbp. So far we have sequenced a couple of fragment libraries with 454 titanium. We now want to sequence some paired-end libraries, but the sequencing facility has problems with getting the titanium 20kbp inserts (and the 8Kbp) to work. 3Kbp inserts seem to work fine, so the question is:
Is there a big difference between 20Kbp and 3Kbp inserts when it comes to the assembly (L50, N50 etc.)?
I have been asking around, and the answer I get is that "of course 20Kbp is better". What I am interested in is how much better it would be (if its worth to wait for x months). These things are difficult to estimate, but if maybe somebody has some experience from similar projects...?
thanks
/Jakub
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