Nanopore bioinformatics & EPI2ME

[AnMa21]

Hello! I've just started a PhD in DNA sequencing for the identification of cancer biomarkers and I was hoping to get some advice on bioinformatic methods. Part of my experimental design is to carry out Nanopore sequencing and I'm quite new to long-read sequencing and bioinformatics. I'd originally planned to use the 'easy' bioinformatic pipeline as advertised by Nanopore so I could practice/learn command line but not miss out on sequencing samples, however I've also noticed its not common to see it in journals or discussions.

Why is this? Would I be unable to publish data analysed with epi2me? Is it better if I sequence the samples THEN carry out bioinformatic analysis when I'm more confident in it?

Thanks!!