Course materials for the NGS analysis course run at icipe, Nairobi.
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README.md

README.md

Bioinformatics approaches to NGS analysis

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)

Monday

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

Tuesday

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

Wednesday

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

Thursday

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

Friday

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

Saturday

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!