Scaffold approach vs make.contigs

Hey there,

our sequencing centre is starting to use 27F anf 519R with the MiSeq 2 x 300 bp. I’ve given some samples a go, and it appears to work i.e. i get contigs and still have > 50 000 seqs a sample. However, at times, I dont trust the data with such low overlap (cue the “why not do the V4 region”).

Would there be any sense to not try and make contigs, but have a forward and reverse read in a scaffold approach i.e. forward sequence information, a (long gap) and reverse sequence information.

Anyone tried this out there?

Unfortunately, I think this is a bad idea and will only lead to headaches. Stick with V4. You and your sequence provider may find this useful…