Ancient Metagenomics
Dates
27-29 May 2025
To foster international participation, this course will be held online
Course overview
The study of ancient microbial, animal, and plant DNA from archaeological samples is a rapidly expanding field with significant potential for uncovering insights into past environments,
lifestyles, and diseases. However, the limited quantity and degraded quality of ancient DNA pose significant challenges to computational analysis. In this course, we will explore the key
challenges and analytical methods in ancient metagenomics, focusing on a comprehensive understanding and practical implementation of the ancient metagenomic workflow, aMeta.
Target audience and assumed background
We assume some basic awareness of UNIX environment, as well as at least beginner level of R and / or Python programming.
Learning outcomes
By completing this course, you will:
- Understand the basics of ancient microbial and environmental metagenomic analysis
- Have an overview of bioinformatic tools and best practices for ancient metagenomic analysis
- Be able to apply aMeta workflow to your ancient metagenomic samples
- Know key challenges, approaches and solutions in the ancient metagenomics research field
- Be able to choose the right tools and approaches to answer your specific research question
Program
Day 1 - 2-8 PM Berlin time
A) Introduction to ancient microbial and environmental metagenomics.
B) Quality control (FastQC, MultiQC), adapter removal (fastp, cutadapt) and taxonomic profiling (Kraken, ngsLCA) of metagenomic reads.
C) Decontamination with negative controls (cuperdec, decontam, recentrifuge) and microbial source tracking (SourceTracker, deCOM). Detecting microbial contamination in eukaryotic databases.
Day 2 - 2-8 PM Berlin time
A) Genome mapping with Bowtie2, BWA and Malt. Learning and interpreting alignment quality metrics and visualizing alignments with IGV.
B) Authentication and validation analysis: damage pattern (mapDamage, PMDtools, MaltExtract, metaDMG), edit distance (MaltExtract) and evenness of coverage.
Day 3 - 2-8 PM Berlin time
A) aMeta ancient metagenomic analysis workflow.
B) De-novo genome assembly (Megahit), taxonomic profiling and authentication of assembled contigs (PyDamage).
Cost overview
Should you have any further questions, please send an email to info@physalia-courses.org
Cancellation Policy:
> 30 days before the start date = 30% cancellation fee
< 30 days before the start date= No Refund.
Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.