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Computational Genomics

Computational Genomics

Rob Edwards via YouTube Direct link

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Computational Genomics

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  1. 1 About Dr. Rob Edwards
  2. 2 Learning Outcomes
  3. 3 Why we are going to use AWS in the course
  4. 4 Create Amazon Web Services Student Account
  5. 5 Start AWS Computational Genomics Image
  6. 6 SSH Keys
  7. 7 Central Dogma
  8. 8 What does it mean to sequence a genome?
  9. 9 What is genome sequencing part 1
  10. 10 What is genome sequencing part 2
  11. 11 Steps In Genome Sequencing
  12. 12 Sanger sequencing
  13. 13 454 pyrosequencing
  14. 14 Introduction to Illumina Sequencing
  15. 15 illumina paired end sequencing
  16. 16 Ion Torrent Sequencing
  17. 17 Pacific Biosciences Sequencing
  18. 18 Oxford Nanopore ONT Sequencing
  19. 19 Definitions
  20. 20 An overview of DNA sequence assembly
  21. 21 Naive DNA sequence assembly
  22. 22 Greedy Assembly of DNA Sequences
  23. 23 Overlap layout consensus sequence assembly approach
  24. 24 de Bruijn graph assembly for DNA sequences
  25. 25 Why does paired end sequencing help assembly?
  26. 26 Assembly problems 1 ... repeats
  27. 27 Assignment1
  28. 28 Assignment 1 solution
  29. 29 Assignment 3
  30. 30 BLAST 1
  31. 31 BLAST 2 seed and extend
  32. 32 BLAST 3 amino acid differences
  33. 33 BLAST 4 PAM vs BLOSUM
  34. 34 BLAST 5 BLOSUM62
  35. 35 BLAST 6 scoring alignments
  36. 36 BLAST 7 scoring gaps
  37. 37 BLAST 8 Probability
  38. 38 BLAST 9 E values
  39. 39 BLAST 10 Algorithms
  40. 40 BLAST 11 PSWM
  41. 41 ESKAPE Pathogens
  42. 42 Klebsiella Introduction
  43. 43 Antibiotics 1 mode of action
  44. 44 Antibiotics 2 mechanisms of resistance
  45. 45 Antibiotics 3 Role of HGT in antibiotic resistance
  46. 46 Antibiotics 4 Resistance Timeline
  47. 47 Antibiotics 5 resistance databases
  48. 48 Subsystems Introduction
  49. 49 Subsystem Classification
  50. 50 Subsystems How to Annotate Genomes and Metagenomes
  51. 51 Introduction to k-mers
  52. 52 Introduction on counting k-mers
  53. 53 k-mer algorithms: Compare and Swap
  54. 54 Bloom Filters
  55. 55 Counting k-mers with Bloom filters
  56. 56 Count Min Sketch
  57. 57 Counting Quotient Filters
  58. 58 Metagenome Binning
  59. 59 CheckM for Genome Consistency
  60. 60 Genome Peek
  61. 61 ABACBS Presentation 2020

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