Benchmarking Guppy algorithms

Fri, 01 Feb 2019 00:00:00 +0000

Methods
Results
Conclusions
Supplementary code {:toc}

ONT’s basecaller Guppy has recently been released to the masses. And with the announcement of the new “flip-flop” basecalling algorithm there is now the choice of two different algorithms for basecalling.

ONT has obviously been singing flip-flop’s praises, and understandably so, as the initial results look like a decent step up in read accuracy.

For an upcoming project I am going to be doing a lot of basecalling of Mycobacterium tuberculosis and given the project will involve assessing metrics heavily reliant on read accuracy I thought it best to invest some time in deciding which algorithm to go with. Another reason for my indecision came when I read a recent blog from Keith Robison which showed that maybe the new flip-flop algorithm doesn’t work well with organisms that have a higher GC content.

Guppy on Microbes made me do it

Benchmarking Guppy algorithms