Nanopore · Plotting · Python

Nanopore sequencing: percent identity over time

My NanoPlot tool includes plots showing the decline in base call quality and sequencing speed over time, see below. Sequencing speed reduction is presumably because the ATP in the fuel mix gets consumed, or pores start wearing out. However, I wondered if this lower quality near the end of the run was also reflected in… Continue reading Nanopore sequencing: percent identity over time

Nanopore · Plotting · Python

PromethION pore count and loading concentration vs yield

Highly similar to my previous post comparing read length and yield on PromethION I today checked the correlation between the pore count on the flow cell and the loading concentration with the yield. The code is highly similar and therefore not shown again. We do not see a strinking correlation between the loading molarity (in… Continue reading PromethION pore count and loading concentration vs yield

Nanopore · Plotting

PromethION sequencing in Antwerp in 2018

We started using PromethION about a year ago, but the good flow cells started arriving from February onwards. Below I have an overview of our runs so far, generated using NanoComp. I’ll blog more about these later if I have the time, but I’m finishing my PhD this month… The plots below show the yield… Continue reading PromethION sequencing in Antwerp in 2018

Coding · Nanopore · Plotting · Python · Uncategorized

Announcing methplotlib: a genome browser for nanopore methylation data

While finalizing my thesis I’ve spend some time on coding methplotlib, a genome browser for nanopore methylation data, currently tailored to nanopolish.  It’s functional but not fully mature. By announcing it now I hope to get some input and feedback on how to improve the system. A screenshot of the end result, for two samples… Continue reading Announcing methplotlib: a genome browser for nanopore methylation data

Nanopore · Plotting · Python

Update on Oxford Nanopore basecall quality scores

Since an older post on basecall quality scores still attracts quite a lot of visits to my blog I think an update is timely. In this post I look at a subset of PromethION data from NA19240, basecalled using Guppy 1.5.1 and aligned to the recommended set of GRCh38 using minimap2 v2.10. Using NanoPlot I… Continue reading Update on Oxford Nanopore basecall quality scores