SPAAM Summer School 2022: Introduction to Ancient Metagenomics Teaching Slides

Teaching slides of the practicals and lectures of the 2022 SPAAM Summer School: Introduction to Ancient Metagenomics (Aug. 1-5 2022).

https://spaam-community.github.io/wss-summer-school/#/2022/

DAY 1

• Lecture Introduction to NGS data: James Fellows Yates
  • What is NGS sequencing and what does its data look like?
• Practical BareBonesBash 1: Aida Andrades Valtueña and Thiseas Lamnidis
  • Introduction to the UNIX command line.
• Practical BareBonesBash 2: Aida Andrades Valtueña and Thiseas Lamnidis
  • How to navigate and batch-manipulate files.
• Round table Introductions
  • Welcome - let's get to know eachother

DAY 2

• Lecture Introduction to ancient DNA: Christina Warinner
  • How to identify and handle DNA from ancient contexts
• Practical Bytesize git: James Fellows Yates and Megan Michel
  • What is git and github? How to clone a repository? What does commit/pull/push mean?
• Practical ancientMetagenomeDir: James Fellows Yates and Megan Michel
  • Where to get ancient metagenomic comparative data, and why is metadata important?
  • Git practice
• Practical nf-core/eager: James Fellows Yates and Megan Michel
  • How do I quality control NGS aDNA data? How do I remove adapters and contamination? How to perform taxonomic profiling?
• Round table Project organisation
  • How to structure my project analysis folders? How to reproducibly document my work?

DAY 3

• Lecture Introduction to Metagenomics: Christina Warinner
  • What are the questions tackled in metagenomics? What are the challenges?
• Practical Introduction to R and the tidyverse / Introduction to Python and Pandas: Clemens Schmid and Nikolay Oskolkov / Maxime Borry and Alex Hübner
  • How to read/write files and run statistical analyses? How to make figures with ggplot2/plotnine
  • (Note: Parallel sessions partcipants can choose which to attend based on their prior experience)
• Practical Taxonomic Profiling, OTU Tables and Visualisation: Maxime Borry and Irina Velsko
  • Python practice. How to normalise OTU tables and perform microbial ecology analyses.
• Round table Taxonomic Classifiers
  • How do I pick a taxonomic classifier? What is best for aDNA?

DAY 4

• Lecture Introduction to microbial genomics: Alexander Herbig
  • How can we learn from studying the genomes of microbes? What questions can we ask?
• Practical Genome mapping: Alexander Herbig and Alina Hiss
  • Why and how do we map against a reference? What parameters are important for aDNA?
• Practical Genome assembly: Alexander Hübner and Nikolay Oskolkov
  • De novo methods for obtaining metagenomically assembled genomes (MAGs). What are the best pipelines and parameters for ancient DNA?
• Roundtable Databases
  • Why are databases so important? What impact does database selection have on my results? What pitfalls should I watch out for?

DAY 5

• Lecture Evolutionary Biology: Sebastian Duchene
  • How have microbes and microbial communities evolved and changed through time? How does this inform our current understanding of the relationships among microbes?
• Practical Phylogenomics: Aida Andrades Valtueña and Arthur Kocher
  • How to perform phylogenetic analysis. What to consider when dealing with low coverage data
• Practical Functional Genomics: Irina Velsko and James Fellows Yates
  • How can we infer genomic function from sequences? What sort of analysis can we do?
• Round table Workshop recap