Genome sequencing with TrueSeq PCR-free 300 or 550 bp?

Question

[User 4014]

Hi folks

We are interested in sequencing genomes of new fungal species, and we think we would use HiSeq 2500 with 150 PE in rapid mode. We are wondering whether TrueSeq PCR-free is suitable for our purpose and which fragment size we shall go for. In term of library prep kit, we have options between PCR-free and Nano, and insert size is either 300 or 550 bp.

Can we have your suggestions please? Our fungi have their genome size between 50-70 Mbases.

Thank you in advance!

Answer 1

[lutz.fr]

I would suggest to look for the read requirements of the assembler you want to use. Why not PE250 bp reads instead of PE150.

The PCR-free kit should generate more complex libraries (compared to nano), but I would prefer a one-tube library prep kit (e.g. Qiagen, BiooScientific, NEB, kapa, Lucigen).