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NERC Advanced Training in Ecological Genomics - Bioinformatics

This repository is part of the NERC Advanced Training in Ecological Genomics taught at the University of Edinburgh in 2023. The documentation contains the bioinformatics part of the training and the files used during the training.

The training consists of the following chapters:

1. Introduction to Linux
2. Quality control and data preprocessing
3. De Novo nuclear genome assembly
4. Plastid assembly
5. Sequence annotation
6. Phylogenetic trees

The training was delivered using Amazon c4.8xlarge (36 CPUs and 60 GiB RAM) VMs. The following tools were installed on the VMs before the start of the training:

• NanoPack
• Redbean
• QUAST
• Minimap2
• Samtools
• ptGAUL
• Plastid Genome Annotator (PGA)
• ugene
• mafft
• Symmetric Alignment-free phylogeNomic Splits (SANS)
• IQTree

Throughout the tutorial, several files are folder were supplied to the students, these files are available for download within this repository.