A (for us) very useful diagnostic of a nanopore run is the status of the pores: if they’re sequencing (‘single_pore’), saturated, unavailable or multiple. It is also interesting to see how fast you are losing pores or killing your flow cell with e.g. a particularly blocky library. Fortunately these metrics are since not-too-long ago saved… Continue reading Comparing the pore status of flow cells
We recently published methplotlib, a tool for the visualization and analysis of modified nucleotides from nanopore sequencing. It works downstream of tools like nanopolish, nanocompore and direct methylation calling by the guppy basecaller. More information can be found on GitHub. Feedback, suggestions, reporting problems and feature requests are very much appreciated. Below are some example… Continue reading Methplotlib examples
Since a recent version of MinKNOW, the software controlling a nanopore sequencer, a sequencing_summary file is created before basecalling, in which one column is of particular interest: the end_reason. Although I’m not yet sure what each value means, I believe it gives per read the reason why the software decided to stop sequencing here, mostly… Continue reading Comparing the end reason of reads in a nanopore experiment
I wanted to make a stacked bar chart to show the number of variants with a certain FILTER status per sample from a multi-sample VCF. Nowadays I make all plots with plotly, because it’s fast, convenient to write and dynamic HTML makes it easier afterwards to select the bits I’m interested in to show. In… Continue reading Stacked bar chart of FILTER information from a multi-sample VCF
Although it was available for a longer time already, in December the long read structural variant (SV) caller SVIM was published as a preprint. As I have published about tools for long read sequencing before I decided to also take a look at SVIM. I started from reads of our NA19240 PromethION genome aligned using… Continue reading Briefly evaluating SVIM
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
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
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
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
I did something very similar to my previous post of a couple of days ago, in which I take the sum of the number of characters of each document in a google drive folder. Today I adapted the code slightly to query individual documents, and added a Class for Documents with a method for counting… Continue reading Getting the number of characters of Google documents
Gigabase or gigabyte 