Nanopore · Plotting · Python

Insertion-deletion ratio in Oxford Nanopore PromethION data

It’s been a while since I wrote another blog post, so here is something short. Today I had to figure out the inversion deletion ratio in Oxford Nanopore Sequencing data from PromethION human whole genome sequencing. I want to compare this ratio for reads which are qualified by albacore as “pass” (average base call quality score… Continue reading Insertion-deletion ratio in Oxford Nanopore PromethION data

Nanopore · Plotting

NanoPlot example gallery update

Months ago I wrote a blog post with an example gallery of plots from NanoPlot so it might be time for an update with NanoPlot v1.9.2 (currently published as a preprint together with my other long read plotting and processing scripts). The data below is from the publicly available NA12878 dataset, release5, base called by the… Continue reading NanoPlot example gallery update

Nanopore · Python

NanoFilt using albacore sequencing_summary for quality filtering

Due to a discrepancy between the quality scores calculated from the reads and those from the sequencing_summary.txt from albacore I added an option to NanoFilt to filter using the qualities specified in the sequencing_summary. NanoFilt now (v1.1.0) also optionally takes a –summary flag for the sequencing_summary file. As a nice bonus, it’s also faster! This added a… Continue reading NanoFilt using albacore sequencing_summary for quality filtering

Nanopore · Plotting

Calculated average quality vs. Albacore summary

I discussed earlier the difference between a) the calculated per read average basecall quality and b) the quality score given by albacore in the sequencing_summary file. Today I had a closer look at this difference and for one dataset I calculated the average quality from the fastq file and compared that to the accompanying sequencing_summary. The… Continue reading Calculated average quality vs. Albacore summary

Nanopore · Plotting

Median basecall quality score to estimate accuracy

I’ve had a few posts already about basecall quality scores and how those compare to the percent identity of the reads. This post is again a short follow-up on those stories. Today I investigate whether the median basecall quality (Phred) score of the aligned fragments is a good or better estimator for the percent identity… Continue reading Median basecall quality score to estimate accuracy

Nanopore · Plotting

The distribution of basecall quality scores

I also investigated the Oxford Nanopore quality scores in some of my previous posts, and this post is a follow-up of those. Today I investigate the distribution of the basecall quality scores and how the mean and median per read behave. At the bottom of this post is the script I used to generate the… Continue reading The distribution of basecall quality scores

Nanopore · Plotting

Averaging basecall quality scores the right way

For my NanoPlot tool, I have been calculating the average basecall quality of a read by simply calculating the arithmetic mean of the Phred scores. I recently also added an option to generate plots based on the sequencing_summary.txt file generated by the albacore basecaller, which completely avoids parsing the fastq file and calculating the mean.… Continue reading Averaging basecall quality scores the right way