Module 5: Genomics

Module topics

  • Genome sequences – sequencing technology and brief NGS overview
  • Genome browsers and annotation
  • Comparative Genomics
  • Human variation

Resources

SessionLecture RecordingsLecture SlidesPractical Assignment
100. Meet the Trainer - Fatma
0. Module5_Session1_Part0
1. Module5_Session1_Part1
2. Module5_Session1_Part2
3. Module5_Session1_Part3
4. Module5_Session1_Part4
5A. Module5_Session1_Part5A
5B. Module5_Session1_Part5B
5C. Module5_Session1_Part5C
6. Module5_Session1_Part6_prac
Module5_Session1

Module5_Session1_prac
Module5_Session1_prac

test_Session1.vcf
21. Module5_Session2_part1
2. Module5_Session2_part2
3.1. Module5_Session2_part3.1
*3.2. Module5_Session2_part3.2
4. Module5_Session2_part4
Module5_Session2Module5_Session2_prac

H3ABioNet_Practical_Task2_GENELIST

H3ABioNet_Practical_Task3_GENELIST

IMPORTANT INFORMATION
31. Module5_Session3_Part1
2. Module5_Session3_Part2
3. Module5_Session3_Part3
4. Module5_Session3_Part4
5. Module5_Session3_Part5
6. Module5_Session3_Part6
Module5_Session3Module5_Session3_prac
41. Module5_Session4_part1
2. Module5_Session4_part2
3. Module5_Session4_part3
4. Module5_Session4_part4
5. Module5_Session4_part5
6. Module5_Session4_part6
Module5_Session4

Module5_Session4_prac
Module5_Session4_prac

H3ABioNet_Genomics_4_Task1

H3ABioNet_Genomics_4_GIAB.vcf_
consolidation sessionModule5_Consolidation_SessionN/AModule5_Consolidation_session_practical

Venter_chr123.vcf

*For session 2, lecture recording 3.2 explains a self-study exercise. Take 10-15 minutes to perform the task outlined in this video before moving on to lecture recording 4

Trainers

Guerfali

 

Fatma Guerfali

Trainer: ‘Genome sequences’ and ‘Comparative Genomics’

Affiliation: Institut Pasteur de Tunis, H3ABioNet

Fatma Guerfali is member of the Laboratory of Transmission, Control and Immunobiology of Infections (LR11IPT02) at Institut Pasteur de Tunis (IPT). Fatma obtained her PhD in Molecular Biology jointly from University Montpellier 2, France and University Tunis El Manar, Tunisia. During her PhD she worked on high-throughput approaches applied to analyse both transcriptomes of infected human macrophages and their different infecting Leishmania strains of contrasted virulences or tropisms. She is currently involved in the generation, analysis, and data mining of high throughput DNAseq, RNAseq, SAGE or microarray data from Leishmania parasites. Her main research interests rely in the analysis of clinical isolates of Leishmania parasites showing differential disease manifestation in human patients and classified according to their associated virulence. The long-term goal is the identification of molecular determinants and genomic variations with a discriminating potential between these parasite isolates as potential drug targets. She has been an invited speaker in several local and international courses and workshops for post-graduates in the field of NGS. Fatma is a member of IPT H3ABioNet node.

Colleen_Saunders

 

Colleen Saunders

Trainer: ‘Genome browsers’ and ‘Human variation’

Affiliation: South African National Bioinformatics Institute, University of the Western Cape

Dr Colleen Saunders is a DST/NRF Innovation Postdoctoral fellow at the South African National Bioinformatics Institute (SANBI) in the Faculty of Natural Sciences at the University of the Western Cape. She has a PhD in Exercise Physiology from the University of Cape Town and her research to date has focussed on genetic risk factors for musculoskeletal soft-tissue injuries such as tendinopathy.