Bioinformatics part 2: Processing fastq files for downstream applications

The following set of videos are a basic introduction of how to process your sequencing data from raw .fast5 files through to what programmes to use for downstream analysis such as creating a phylogenetic tree. The tutorials provide information on some programmes and commands that you can use to process your Oxford Nanopore data. For further information and to download the accompanying PDF, please visit https://pandora.tghn.org/sequencing/s...

In this section we cover how to process your raw sequencing reads so that you can then assemble them, as well as an introduction to quality control checks. This section includes the basic code required to run the commands with the following programmes:
- An introduction to Guppy, including basecalling, demultiplexing, trimming and concatenating files
- Introduction to checking the quality of your data, including using the programmes FastQC and MultiQC
- Using EPI2ME Labs for QC

Apologies for the poor sound quality in parts of the video