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

Trimming and filtering Oxford Nanopore sequencing reads

I recently wrote NanoFilt, a script for filtering and trimming of Oxford Nanopore sequencing data. The script reads from stdin, performs trimming and sends output to stdout. As such it can easily get integrated into your pipeline using pipes. All parameters are optional, so the reads are left unchanged when no flags are set. Filtering… Continue reading Trimming and filtering Oxford Nanopore sequencing 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

Adding a progress bar to albacore

Albacore is software from Oxford Nanopore Technologies to perform basecalling of the reads obtained by their sequencers. Since the wrapper script is written in Python I can adapt it, and I wanted to try to add a progress bar to the script and that turned out to be surprisingly easy. Obviously, there was no need to reinvent… Continue reading Adding a progress bar to albacore

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