Guppy 2.1.3 "normal mode" vs. "flip-flop" mode

A follow-up to Keith Robinson's "Flappie vs. Albacore via Counterr" blog post

TL;DR Guppy 2.1.3 using GPU is blazing fast. No matter if you run it in the "normal" or "flip-flop" mode. Flip-flop was quite a bit slower though, but still OK. I do not see major improvements using flip-flop mode. Flip-flop gives me a strange Q-score distribution. But this is still a pre-release, so I expect some (major?) improvements over the next months.

Long version

This post is a quick follow-up to this blog post by Keith Robinson where he compared Albacore vs. Flappie. In this post I am going to compare Guppy 2.1.3 normal mode vs. Guppy 2.1.3 flip-flop mode. Flip-flop was announced by Clive G. Brown in this talk.

First let me say that this is no in depth analysis and comparison of the two Guppy modes. I did this for internal testing.

Here some background:

• I used this assembly as a reference (Let's call it reference sequence quality. It is assembled using ONT and polished with Illumina)
• This is the raw ONT data. Not the newest, but it is sequenced with R9.5
• I installed Guppy 2.1.3 from a .deb package provided by ONT. It is run on AWS EC2 as shown here.
• Mapping performed using minimap2-2.14
• The analysis was done with counterr