Monday, 12-6 pm Berlin time
- Presentation and course overview.
- Introduction to NGS and ancient DNA: the paleogenomic era
- Theoretical background on metagenomic analysis.
- 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
- Raw data pre-processing and reads mapping theoretical backgroung.
- The SAM and BAM formats.
- 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
- Deaminations and DNA damage assessment, contamination and data authentication.
- the VCF format and variant calling theoretical background.
- DNA damage assessment (MapDamage, PMDtools).
- Variant calling and filtering (Samtools-bcftools, GATK HaplotypeCaller).
Thursday, 12-6 pm Berlin time
- Introduction to phylogenetic analysis.
- From vcf file to sequence alignment and phylogenetic tree reconstruction.
- 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
- Final recap and discussion
- Class project: Using acquired knowledge to explore ancient human NGS data from reads mapping to SNPs calling.