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Genomic Methods
Genomic Methods

Linux Intro

  • Introduction to Linux and working on the command line
    • 0 Learning goals
    • 1 First steps
    • 2 Basic commands
    • 3 Additional reading

HPC intro

  • HPC Intro
    • Connect to the cluster
    • Meet the cluster
    • Submit jobs
    • Conda and Snakemake

Genome Assembly

  • Genome Assembly
    • Preparation
    • Illumina data basics
    • Read trimming
    • Read merging
    • K-mer counting
    • De novo assembly

Post Assembly

  • Post Assembly
    • Introduction
    • Post-assembly analyses

Phylogenomics

  • Phylogenomics
    • Introduction
    • Practical start

Sequence databases

  • Sequence Databases
    • Setup
    • Nucleotide sequence databases
    • Sequence alignment and BLAST
    • BLAST on the command line
    • Other alignment tools
    • Final task

Metabarcoding databases

  • Metabarcoding Databases
    • Setup
    • Introduction
    • Reference databases
    • Case study
    • QIIME environment

Functional annotation databases

  • Functional Annotation Databases
    • Setup
    • Introduction
    • Genome annotation concepts
    • Databases and tools
    • Pathway analysis and Gene Ontology
    • Annotation case study
    • Enrichment analysis

Reproducibility Fundamentals

  • Reproducibility Fundamentals
    • Overview
    • Working environment
    • Day 1: command line, software, data, Git
    • Day 2: environments and containers
    • Day 3: workflows and pipelines
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