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@@ -24,7 +24,7 @@ Lectures and Practical sessions are typically 2 hours, and round-table discussio
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-**Lecture** Introduction to NGS data: _James Fellows Yates_
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- What is NGS sequencing and what does its data look like?
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-**Practical** BareBonesBash: _Aida Andrades Valtueña and Thiseas Lamnidis_
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-**Practical** BareBonesBash: _Thiseas Lamnidis and Aida Andrades Valtueña_
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- Introduction to the UNIX command line.
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-**Practical** Introduction to R and the tidyverse / Introduction to Python and Pandas: _Clemens Schmid and Keri Burge_ / _Rémi Denise and Freya Steinhagen_
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- How to read/write files and run statistical analyses? How to make figures with ggplot2/plotnine
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- How can we learn from studying the genomes of microbes? What questions can we ask?
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-**Practical** Genome assembly: _Alex Hübner and Jasmin Frangenberg_
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- De novo methods for obtaining metagenomically assembled genomes (MAGs). What are the best pipelines and parameters for ancient DNA?
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-**Practical** Phylogenomics: _Arthur Kocher and Aida Andrades Valtueña_
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-**Practical** Phylogenomics: _Aida Andrades Valtueña and Megan Michel_
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- How to perform phylogenetic analysis. What to consider when dealing with low coverage data
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-**Round table** Instructor open hours
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- An opportunity for students to ask the instructors any questions about the content they have learnt so far, or to get advice on their own research.
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-**Lecture** Introduction to eDNA: _Vilma Pérez_
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- How have microbes and microbial communities evolved and changed through time? How does this inform our current understanding of the relationships among microbes?
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-**Practical** Authentication and Decontamination (microb(iom)es): _Nikolay Oskolkov, Freya Steinhagen, and James Fellows Yates_
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-**Practical** Authentication and Decontamination (microb(iom)es): _Nikolay Oskolkov, Freya Steinhagen_
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- How can I validate my DNA is ancient? What sort of analyses can convince ourselves and a reviewer we have good preservation?
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-**Practical** Authentication and Decontamination (eukaryotes): _Giulia Zampirolo and James Fellows Yates_
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- How can I validate my DNA is ancient? What sort of analyses can convince ourselves and a reviewer we have good preservation?
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-**Practical** Ancient Metagenomic Pipelines: _Nikolay Oskolkov, James Fellows Yates_
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- What pipelines exist for specifically ancient DNA and ancient metagenomic data?
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-**Practical** Ancient Metagenomic Pipelines: _James Fellows Yates and Nikolay Oskolkov_
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- What pipelines exist for specifically ancient DNA and ancient metagenomic data, e.g. nf-core/eager, aMeta, and nf-core/mag?
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- 2025: How to run nf-core/eager
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-**Round table** (Leipzig only) Dinner for Students and Instructors.
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