# 0.1 BMMB554

- [Syllabus](/I1cr74ygROOjymoAYgPneQ)

Block 1
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- [**1.1.** Class Intro + Google Colaboratory](/FGSFU6m7Q2auzWlSRZBRsA)
- [**1.2.** A quick Python refresher](/wr1u1vTXQr2RfTngFLRi8g)
- [**1.3.** Pandas I: Basics](/w2lsCfIYR4ah3jI5Cl7zKQ)
- [**1.4.** Pandas II: Wide versus long, split-apply-combine and more ...](/-A9UuB1wRNeFlTLFCj4XeA)
- [**1.5.** Plotting I: High level versus low plotting. Bokeh](/@0nj-AtnfQ3KFSqVrfVLhvw/r1No0l8g_)
- [**1.6.** Plotting II: Building a mini genome browser](/@0nj-AtnfQ3KFSqVrfVLhvw/S1soFOtgu)
- [**1.7.** Introduction to Galaxy I](/@0nj-AtnfQ3KFSqVrfVLhvw/ryF2iINZu)

Block 2
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- [**2.1.** History of sequencing and begining of NGS](/UcyDNXmBRR-dCHQQ5WgZiw)
- [**2.2.** Illumina](/yK4xRBphQFKRboZ23sKSHw)
- [**2.3.** PacBio](/9BVkSP9OQVCSVXPRv727sA)
- [**2.4.** Oxford Nanopore](https://hackmd.io/mPtV0OyuSgyDoU05d6mdiA)
- [**2.5.** Some exotic stuff](/c2LSZb06SeOYvzczgmCLWg)

Block 3
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- [**3.1.** Assembly I: Finding the data](/pjyLaz_tTpuZpKX4ufxtAw)
- [**3.2.** Assembly II: *k*-mers and graphs](/pxXFPpaXSIyBDgqe_Wf0hQ)
- [**3.3.** Assembly III: examples](/83H5__QETIWsyDfQ7NfjWQ)
- [**3.4.** Finding matches quickly](/b_TOZCxUSpiJn43MnGDtQQ)
- [**3.5**. Sequence alignment](/ti_bDxQdTM-MNjT7hgEMuA)

Block 4
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- [**4.1.** Project discussion](/iNB4ZreyQMKd4YJX2CVR0w)
- [**4.1.1** Project 1: Market Basket Analysis](/9sOTf-mcT96Y3ESN39hjug)
- [**4.1.2** Project 2: Up-to-date VOC lists](/tmGa0PSHRV-X0ci8bQl-Ig)
- [**4.1.3** Project 3: Low AF sites: Real or Not?](/Q8saBOQHRIatuI7wI7vF9A)
- [**4.2** Varinat Calling I: Diplod case](/8m1-Dm-0SDWnNTUl0ZyGkg)
- [**4.3** Variant calling II: Haploid case](/zfOO-eSZQEGhGPAxLRDQ7w)