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/sequencing-tutorials/
In this section we cover how to assemble your sequencing files to create an assembly (or contigs). This section includes the basic code required to run the commands with the following programmes:
- Aligning your sequencing files using a reference genome (using MiniMap2)
- Assembling a de novo genome (using Flye)
- Using EPI2ME Labs to assemble a genome
- Genome polishing (using Medaka)
- Genome quality assessment (using Promoxis)
Apologies for the poor sound quality in parts of the video, presented by @linzyelton4592
