# Lecture slides 2024


###### Day 1

[Welcome and practical information (TR)](D01T0915-Welcome_and_practical_information-TR-2024.pdf)

[Sequencing and applications (TR)](D01T1315-Sequencing_and_applications-TR-2024.pdf)

[Fundamentals of molecular biology 1: A guided tour of the (human) genome (RS)](D01T0930-20241028_I_GuidedTourOfHumGenome.pdf)

[Fundamentals of molecular biology 2: From DNA to biological function (RS)](D01T0930-20241028_II_FromDNA2BiologicalFunction.pdf)

[Fundamentals of molecular biology 3: Genomics in biomedical research (RS)](D01T0930-20241028_III_GenomicsInBiomedicalResearch.pdf)

[Illumina sequencing technology (AS)](D01T1415-Illumina-AS.pdf)

[PacBio sequencing technology (ATK)](D01T1515-241028_IN_BIOSx000_ATK.pdf)


###### Day 2

[Introduction to Nanopore sequencing (TH)](D02T0915-20241029-Introduction_to_Nanopore_sequencing.pdf)

[Library preparation (AS)](D02T1015-Library-preparation-AS.pdf)

[Experimental design (AS)](D02T1115-Experimental-design-AS.pdf)

[Basic file formats (AS)](D02T1315-Basic-file-formats-AS.pdf)

[Access to computational resources (TR)](D02T1415-Access_to_computational_resources-TR-2024.pdf)


###### Day 3

[Data preprocessing (AS)](D03T0915-Data-processing-AS.pdf): [Exercises](D03T0915-Data_preprocessing-AS-handson.txt)

[Introduction to containers (AS)](D03T1115-Containers-AS.pdf)

[Introduction to analysis pipelines with Nextflow (AS)](D03T1315-Nextflow-AS.pdf)

[Introduction to Snakemake (EBB)](D03T1415-Snakemake-EBB.pdf)


###### Day 4 and 5

*De novo* genome assembly (KL) [Part 1](D04T0915-Assembly1-KL-2024.pdf), [Part 2](D04T0915-Assembly2-KL-2024.pdf), [Part 3](D04T0915-Assembly3-KL-2024.pdf), [Part 4](D04T0915-Assembly4-KL-2024.pdf), [Exercises](https://github.com/karinlag/BIOS9000/tree/2024)


###### Day 6

[Introduction to variant calling (BS)](D06T0915-Intro-SNP-calling-BS.pdf): [Exercises](D06T0915-Intro-SNP-calling-Exercises-BS.pdf) [Answers](D06T0915-Intro-SNP-calling-Answers-BS.pdf)

[Human germline variant calling (YS)](D06T1515-Variant-calling-YS-2024.pdf)


###### Day 7

[Somatic variant calling and interpretation in the context of cancer (SN)](D07T1315-Somatic-variant-calling-SN-2024.pdf)

###### Day 8

[Microbiome sequencing and analysis (NKN)](D08T0915-Microbiome-sequencing-NKN-2024.pdf)

[Multi-omic network analysis (NKN)](D08T1315-Network-Analysis-NKN-2024.pdf)


###### Day 9

[Introduction to RNA-Seq (AS)](D09T0915-RNA-seq-AS-2024.pdf)

[Small RNA transcriptomics (TBR)](D09T1015-Small-RNA-Seq-TBR-2024.pdf): [Exercises](D09T1015-Small-RNA-Seq-Exercises-TBR-2024.pdf)


###### Day 10

[Machine learning in computational biology (MP)](D10T0915-Machine-learning-MP-2024.pdf)