Goal

To generate QC reports using NanoPlot.

Background

Quality control of sequencing data is pivotal to ensure high quality downstream analyses such as genome assembly, typing, and annotation. If the quality of the sequencing data is low or if it contains contaminants the conclusions drawn based on downstream analyses can be wrong.

Practical

In this exercise we are going to use the command line tool NanoPlot to perform quality control on Nanopore sequencing data.

We will run the analysis on isolate Ec001 today and examine the output in Session 2 on Thursday.

NanoPlot is developed by Wouter De Coster and is a tool for summarizing and plotting long-read sequencing data.

Instructions

We assume that you have installed NanoPlot prior to the course but if not, you can find installation instructions and usage help on Github:

wdecoster/NanoPlot: Plotting scripts for long read sequencing data (github.com)

1. Locate the long-read sequencing data for Ec001 that you downloaded at the beginning of the Session.

2. Go to where you have NanoPlot installed and look at the help message by typing:

NanoPlot -h

Inspect the help message and consider which options are essential.

• NanoPlot takes many different types of input files. What type of input are we working with?

• Do you want to specify an output directory?

• Anything else?

3. Run NanoPlot. You can run the simple command shown below but try to add more options.

(This should take a few minutes depending on the number of cores you have available.)

NanoPlot --fastq [Ec001_fastq_reads]

4. NanoPlot should now have generated a bunch of output files which we will examine further in Session 2.