Nanopore · Plotting

Per base sequence content and quality (end of reads)

After my earlier posts investigating the sequence content and quality at the start of Oxford Nanopore sequencing reads, I also wanted to include some code to look at the end of reads. These functions are part of the unfinished tool nanoQC, in which I want to replicate some of the plots made by FastQC. Creating the same plots as… Continue reading Per base sequence content and quality (end of reads)

Nanopore · Plotting

Example gallery of NanoPlot

I am developing NanoPlot, a python package for plotting various aspects of Nanopore sequencing data (fastq) and alignments (bam). It’s a python script, heavily using the seaborn package for creating plots. The package is available on GitHub and I welcome all feedback and suggestions! In this post, I will show some examples of plots. The data is… Continue reading Example gallery of NanoPlot

Nanopore · Plotting

Per base sequence content and quality (new basecaller)

A few weeks ago I blogged about the Per base sequence content and quality in nanopore sequencing data, which was performed on data from an earlier iteration of the basecalling tool. A newer version of Albacore (v1.0.4) incorporating a transducer (Scrapie) was released some time ago, and I recently upgraded our installation to v1.1.0. The main… Continue reading Per base sequence content and quality (new basecaller)

Nanopore · Plotting

Per base sequence content and quality

I wrote a script to produce QC plots analogous to the “Per base sequence quality” and ”Per base sequence content” from FastQC for Nanopore sequencing data. Since there is no fixed read length this representation is less straightforward, so it’s necessary to make a selection of the data. My script starts from a fastq file, which I… Continue reading Per base sequence content and quality

Nanopore · Plotting

Getting the edit distance from a bam alignment: a journey

A relevant parameter when looking at sequencing and alignment quality is the edit distance to the reference genome, roughly equivalent to the accuracy of the reads. (Roughly, because we ignore true variants between the sample and reference). The edit distance or Levenshtein distance can be defined as the number of single letter (nucleotide) changes that have to… Continue reading Getting the edit distance from a bam alignment: a journey

Nanopore · Plotting

Nanopore ActivityMaps

In February Keith Robison suggested in his post Could Hermione Tackle MinION Yield Variability? it would be useful to get a physical overview of the sequenced reads per channel. This script should visualise which channels have been very productive and which didn’t contribute at all. I thought this was a neat idea, and since I am working on a… Continue reading Nanopore ActivityMaps