Nanopore

LRGE (pronounced “large”) estimates genome size directly from long read sequencing data, without assembling the reads into a genome first. We published the paper in 2025 [1], and since then I’ve been working on cases where its estimates go wrong. Those changes are now available in version 1.0.0. The biggest changes are depth normalisation and more selective filtering of internal matches caused by repeats. Getting those working also led to improvements in runtime and memory use, and uncovered a bug that had been affecting every PacBio estimate. ...

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. ...