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)

Uncategorized

Oxford Nanopore basecall quality scores

A recent switch in Oxford Nanopore basecaller software (albacore v1.0.1) substantially improved the per-base quality scores, as mentioned in a previous post. I wondered if those quality scores are accurate. As shown below, the average base quality of a read is above 16. These scores are Phred-scaled quality scores, meaning they correspond to the -10*log10(Probability of incorrect… Continue reading Oxford Nanopore basecall quality scores

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