Monday, 12-6 pm Berlin time

 

 

Lecture:

 

- Presentation and course overview.

 

- Introduction to NGS and ancient DNA: the paleogenomic era

 

- Theoretical background on metagenomic analysis.

 

 

Hands-on:

 

- Introduction to Unix: basic and advanced command line concepts.

 

- Metagenomic screening of ancient samples (e.g. Metaphlan, Kraken, Krona)

 

 

 

 

Tuesday, 12-6 pm Berlin time

 

 

Lecture:

 

- Raw data pre-processing and reads mapping theoretical backgroung.

 

- The SAM and BAM formats.

 

 

Hands-on:

 

- Quality control, trimming and filtering of raw-seqencing data (e.g. FastQC, AdapterRemoval, ClipAndMerge).

 

- Alignment of reads to a reference genome and data visualization (BWA, Picard, GATK, IGV)

 

 

 

 

Wednesday, 12-6 pm Berlin time

 

 

Lecture:

 

- Deaminations and DNA damage assessment, contamination and data authentication.

 

- the VCF format and variant calling theoretical background.

 

 

Hands-on:

 

- DNA damage assessment (MapDamage, PMDtools).

 

- Variant calling and filtering (Samtools-bcftools, GATK HaplotypeCaller).

 

 

 

 

Thursday, 12-6 pm Berlin time

 

 

Lecture:

 

- Introduction to phylogenetic analysis.

 

- From vcf file to sequence alignment and phylogenetic tree reconstruction.

 

 

Hands-on:

 

- vcf files pre-precessing for phylogenetic analysis.

 

- Building a phylogenetic tree (PhyML, IQ-TREE, ModelFinder), data visualization and discussion.

 

 

 

 

Friday, 12-6 pm Berlin time

 

 

Lecture:

 

- Final recap and discussion

 

 

Hands-on:

 

- Class project: Using acquired knowledge to explore ancient human NGS data from reads mapping to  SNPs calling.