Nextera Prep for AT rich template (P. falciparum)

[Orome]

Hey guys,
it's my first post in that great forum of yours so correct me if I'm doing anything wrong. Following situation:
We want to sequence P. falciparum (23 Mb) on a MiSeq with Nextera XT library prep. I have not worked with falciparum before but literature says that its extremely at-biased genome makes library prep difficult because the Illumina polymerase does not effectively amplify AT-rich regions which results in uneven coverage. They suggest adding TMAC to the PCR and using Kapa Hifi as polymerase. However the paper is from 2012 and they did not use the Nextera Kit.
So my question is, has anyone experience with sequencing falciparum and/or has experience with tweaking the Nextera Kit.

Thanks a lot.

Orome

[Markiyan]

Use PCR-Free library preps for high AT.

Based on my experience and some publications I would strongly recommend doing a PCR-free library prep.
(Use Illumina or Lucigen PCR-free kit).

While it is possible to improve coverage on high GC regions by tweaking the reaction/cycling conditions, the high AT ones are much less amenable to it...

So use a PCR-free method or at least minimise the number of cycles.

[thermophile]

I haven't worked with high AT, but from my experience with high GC genomes I'd recommend truseq over nextera. The "random" cleaving is clearly not random in genomes that aren't typical