# Lecture slides 2022

###### Day 1
* [Day 01: Welcome and practical information (TR)](Day%2001.1%20-%20Welcome%20and%20practical%20information%20-%20TR.pdf)
* [Day 01: Fundamentals of molecular biology part 1 (RS)](Day%2001.2%20-%20Fundamentals%20of%20molecular%20biology%20part%201%20-%20RS.pdf)
* [Day 01: Fundamentals of molecular biology part 2 (RS)](Day%2001.3%20-%20Fundamentals%20of%20molecular%20biology%20part%202%20-%20RS.pdf)
* [Day 01: Fundamentals of molecular biology part 3 (RS)](Day%2001.4%20-%20Fundamentals%20of%20molecular%20biology%20part%203%20-%20RS.pdf)
* [Day 01: Sequencing and applications (TR)](Day%2001.5%20-%20Sequencing%20and%20applications%20-%20TR.pdf)
* [Day 01: Illumina sequencing technology (AS)](Day%2001.6%20-%20Illumina%20sequencing%20technology%20-%20AS.pdf)
* [Day 01: PacBio sequencing technology (ATK)](Day%2001.7%20-%20PacBio%20sequencing%20technology%20-%20ATK.pdf)

###### Day 2
* [Day 02: Oxford Nanopore sequencing technology (TH)](Day%2002.1%20-%20Oxford%20Nanopore%20sequencing%20technology%20-%20TH.pdf)
* [Day 02: Library preparation (AS)](Day%2002.2%20-%20Library%20preparation%20-%20AS.pdf)
* [Day 02: For all you seq - DNA](for-all-you-seq-dna.pdf)
* [Day 02: For all you seq - RNA](for-all-you-seq-rna.pdf)
* [Day 02: Experimental design (AS)](Day%2002.3%20-%20Experimental%20design%20-%20AS.pdf)
* [Day 02: Basic file formats (AS)](Day%2002.4%20-%20Basic%20file%20formats%20-%20AS.pdf)
* [Day 02: Access to computational resources (TR)](Day%2002.5%20-%20Access%20to%20computational%20resources%20-%20TR.pdf)

###### Day 3
* [Day 03: Data preprocessing (AS)](Day%2003.1%20-%20Data%20preprocessing%20-%20AS.pdf)
* [Day 03: Data preprocessing script (text file) (AS)](Day3_1_DataPreprocessing_script.txt)

###### Day 4
* [Day 04: *De novo* genome assembly - Course material on GitHub (KL)](https://github.com/karinlag/BIOS9000/tree/2022)
* [Day 04: Principles and problems of *de novo* genome assembly (KL)](Day%2004.1%20-%20De%20novo%20genome%20assembly%20-%20KL.pdf)
* [Day 04: Genome assembly programs - how do they work? (KL)](Day%2004.2%20-%20SPAdes%20and%20Velvet%20assemblers%20-%20KL.pdf)

###### Day 5
* [Day 05: QUAST assembly evaluation (KL)](Day%2005.1%20-%20QUAST%20-%20KL.pdf)

###### Day 6
* [Day 06: Introduction to variant calling (BS)](Day%2006.1%20-%20Introduction%20to%20variant%20calling%20-%20BS.pdf)
* [Day 06: Variant calling: Walrus mitochondrial genome exercise (BS)](Exercise_walrus_mt_genome_SNP_Calling.pdf)
* [Day 06: Human variant calling - Lecture (YS)](Day%2006.2%20-%20Human%20variant%20calling%20-%20YS.pdf)
* [Day 06: Human variant calling - Exercise procedure (YS)](Procedure.txt)

###### Day 7

* [Day 07: Somatic variant calling (SN)](Day%2007.1%20-%20Somatic%20variant%20calling%20-%20SN.pdf)

###### Day 8

* [Day 08: Statistical genomics (IG)](Day%2008.1%20-%20Statistical%20genomics%20-%20IG.pdf)

###### Day 9
* [Day 09: Small RNA transcriptomics lecture (TBR)](Day%2009.1%20-%20RNA%20transcriptomics%20lecture%20-%20TBR.pdf)
* [Day 09: Small RNA transcriptomics practicals (TBR)](Day%2009.2%20-%20RNA%20transcriptomics%20practicals%20-%20TBR.pdf)

###### Day 10
* [Day 10: Machine learning in computational biology (MP)](Day%2010.1%20-%20Machine%20learning%20in%20computational%20biology%20-%20MP.pdf)