TrueSeq PCR free vs Nextera Mitogenome seq

[frascom]

I wondered if anyone had any recommendations for TrueSeq PCR free kits vs Nextera XT for mitogenome sequencing around 17,000bp pooling PCR fragments and around 192 individual samples on a single Miseq run?

Are there benefits of considering one over the other or protocols to follow for sample size and barcoding

thanks for the help

[SNPsaurus]

Can you multiplex that much on a Miseq and get enough reads per sample to reconstruct the mitogenome? I guess if the nuclear genome isn't large then a reasonable fraction of reads will go to the mitogenome.

You can use partial reaction of just Nextera DNA Flex and get good results. That might be the cheapest route.

[frascom]

I have amplified the mitogenome separately so there should no concern of reads. The main aim is trying to save some costs due to barcoding 192 individuals whilst achieving a high quality of reads. The benefit of NexteraXT I think is the availability of barcodes index for up to 384 samples. Although another option would be to use propriety barcodes so save a lot of money

[SNPsaurus]

I see, that makes sense for amplified mtDNA.

You can combine the Nextera Flex and Nextera XT barcode sets for Nextera Flex preps. We do that for increased multiplexing.

[nucacidhunter]

plexWell 96 or 384 could fit your library prep. It seems to be cheap and also quick.

https://seqwell.com/product/pw96/