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!
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!
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