Course materials for the NGS analysis course run at icipe, Nairobi.
The main course webpage is here.
Course Programme Bioinformatics approaches for NGS analysis course, ICIPE, Nairobi, 30th Nov - 2014.
Instructors:
- Jelena Aleksic (TReND in Africa)
- Benard Kulohoma (icipe)
- Mark Wamalwa (BecA-ILRI Hub, Nairobi, Kenya)
- Richard Smith-Unna (University of Cambridge)
- Simon Martin (university of Cambridge)
- Risha Govind (Imperial College London)
- Rosaline Macharia icipe, Nairobi, Kenya)
- Kelvin Muteru (icipe)
- Sarah Hoey (Mendeley)
| Time | Subject | |
|---|---|---|
| 0845 - 0915hrs | Introductions and Welcome | BK, JA |
| 0915 - 1000hrs | Introduction to big data | RM |
| 1000 - 1040hrs | Overview of different types of next generation sequencing | KM |
| Break | ||
| 1100 - 1300hrs | Unix basics | MW |
| Lunch | ||
| 1400 - 1530hrs | Introduction to R | JA |
| Break | ||
| 1600 - 1730hrs | Small groups project time |
| Time | Subject | |
|---|---|---|
| 0900 - 0945hrs | Introduction to genomics experimental design | JA |
| 0945 - 1030hrs | Introduction to NGS analysis methods | RSU |
| Break | ||
| 1100 - 1230hrs | Practical: Unix and shell scripting | MW |
| Lunch | ||
| 1330 - 1530hrs | Practical: R data structures | JA |
| Break | ||
| 1600 - 1700 | Practical: Mendeley, literature management and social media | SH |
| 1700 - 1800hrs | Small groups project time |
| Time | Subject | |
|---|---|---|
| 0900 - 0945hrs | Approaches to sequence mapping and genotyping | SM |
| 0945 - 1030hrs | Approaches to transcriptome analysis | JA,MW |
| Break / View Inqaba Biotec displays | ||
| 1100 - 1300hrs | Practical: RNAseq QC and differential expression analysis | JA,MW |
| Lunch / View Inqaba Biotec displays | ||
| 1400 - 1530hrs | Mentoring sessions | JA |
| Break / View Inqaba Biotec displays | ||
| 1600 - 1700hrs | Inqaba Biotec - East Africa | |
| 1700 - 1800hrs | Small groups project time | |
| 1900hrs | Course dinner |
| Time | Subject | |
|---|---|---|
| 0900 - 0945hrs | De novo sequence assembly | RSU |
| 0945 - 1030hrs | Plant synthetic biology | RSU |
| Break | ||
| 1100 - 1300hrs | Practical: De novo sequence assembly | BK |
| Lunch | ||
| 1400 - 1530hrs | Practical: Data visualisation in R using ggplot2 | RSU |
| Break | ||
| 1600 - 1730hrs | Small groups project time |
| Time | Subject | |
|---|---|---|
| 0900 - 0930hrs | [Introduction to GWAS and Variant Calling]) | RG |
| 0930 - 1030hrs | Practical: From raw reads to aligned data | RG |
| Break | ||
| 1100 - 1200hrs | Practical: From aligned data to Variants called | RG |
| Lunch | ||
| 1400 - 1530hrs | Practical: Filtering Variants | RG |
| Break | ||
| 1600 - 1730hrs | Small groups project time |
| Time | Subject | |
|---|---|---|
| 0900 - 0945hrs | [Evolutionary genomics analysis approaches]) | SM |
| 0945 - 1030hrs | Introduction to comparative genomics approaches | SM |
| Break | ||
| 1100 - 1200hrs | Practical: Multiple sequence alignment and cross species comparisons | SM |
| Lunch | ||
| 1230 - 1400hrs | Practical: Population genetics | SM |
| 1400 - 1500hrs | Student presentations about research projects. 10 mins per group for presentation and questions. | |
| Break | ||
| 1530 - 1600hrs | Informal course discussions and certificate presentation and vote of thanks! |
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