Programme

Advanced Genomics and Bioinformatics Training Workshop BecA-ILRI Hub, ILRI Campus, 7th -19th August 2016

TIME ACTIVITY ROOM RESOURCE PERSONS

SUNDAY 7 AUGUST 0800 – 0830 Arrival and Registration JVC Joyce Nzioki

Marvin Wasonga / Dedan Githae 0830 – 0900 Welcome and workshop opening

• Welcome remarks • Overview of BecA-ILRI hub and capacity building

program • 10 years SLU-BecA Partnership • Self introduction by trainers • Self introduction by participants

JVC Wellington Ekaya (Senior Scientist - Capacity Building) Appolinaire Djikeng (Director BecA-ILRI Hub) Eric Bongkam - SLU (Photography; Marvin Wasonga)

0900 - 0915 Pre-Workshop Test JVC Joyce Njuguna / Dedan Githae 0915 – 0945 Lecture: Introduction to Genomics (The capacity at BecA ) JVC Francesca Stomeo 0945 – 1030 Lecture: Illumina Library Preparation JVC Walter Verweij 1030 – 1045 Tea Break and Group Photo JVC Marvin Wasonga 1045 – 1115 Health and Safety Talk JVC EOHS Representative 1115 – 1300 Laboratory: Nextera DNA Library prep

Presequencing Quality Control (quality/quantity) DNA Quantification

Lab4 Walter Verweij, Francesca Stomeo, Tilly Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

1300 – 1400 Lunch Cafeteria 1400 – 1700 Laboratory: Nextera DNA Library prep

Tagmentation of Genomic DNA

Lab4 Walter Verweij, Francesca Stomeo, Tilly Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

MONDAY 8 AUGUST 0800 – 0830 Outline of day 2 activities JVC Dedan Githae and Joyce Nzioki 0900 – 1100 Laboratory: Nextera DNA Library prep

Library amplification and clean-up Lab4 Walter Verweij, Francesca Stomeo, Tilly

Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

1100 – 1115 Tea Break JVC 1115 – 1300 Laboratory: Nextera DNA

Library Quantification Lab4 Walter Verweij, Francesca Stomeo, Tilly

Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

1300 – 1400 Lunch Cafeteria 1400 – 1530 Laboratory: Nextera DNA Library prep

Library quality control Lab4 Walter Verweij, Francesca Stomeo, Tilly

Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

1530 - 1545 Tea Break JVC 1545 – 1700 Laboratory: Nextera DNA Library prep

Finish of Lab Work Lab4 Walter Verweij, Francesca Stomeo, Tilly

Eldridge, Eunice Machuka, Pauline Asami, Collins Mutai, Vincent Njunge

TUESDAY 9 AUGUST

0800 – 0830 Outline of day 2 activities JVC Dedan Githae / Joyce Nzioki 0830 - 0900 Key Note Speaker I JVC 0900 – 1100 Introduction to Statistics:

• Introduction to R and Rstudio JVC

Stephen Opiyo 1100 – 1115 Tea Break JVC 1115 – 1300 Introduction to Statistics:

• Descriptive statistics • Hypothesis testing • Parametric statistics (T-Test and ANOVA)

JVC Stephen Opiyo

1300 – 1400 Lunch Cafeteria 1400 – 1530 Introduction to Statistics:

• Non-parametric statistics (Mann-Whitney U test and Kruskal-Wallis)

• Correlations

JVC Stephen Opiyo

1530 - 1545 Tea Break JVC 1545 – 1800 Introduction to Statistics:

• Introduction to regression • Hands on: Statistical Analysis using R/Rstudio

JVC Stephen Opiyo

WEDNESDAY 10 AUGUST 0800 – 0830 Outline of day 3 activities JVC Dedan Githae and Joyce Nzioki 0830 – 0915 Lecture: Introduction to Bioinformatics

JVC Eric Bongcam

0915 - 1000 Lecture: Introduction to LINUX JVC James Oguya, Dedan Githae, Joyce Nzioki 1000 – 1015 Tea Break JVC 1015 – 1300 Hands-on: Command line Linux

JVC James Oguya, Dedan Githae, Joyce Nzioki

1300 – 1400 Lunch Cafeteria 1400 – 1600 Hands-on: Command line Linux

JVC James Oguya, Dedan Githae, Joyce Nzioki

1600 - 1615 Tea Break JVC 1615 – 1800 Hands on: Command line Linux JVC James Oguya, Dedan Githae ,Joyce Nzioki

THURSDAY 11 AUGUST 0800 – 0830 Outline of day 4 activities JVC Dedan Githae and Joyce Nzioki

0830 – 0930 Lecture: Introduction to Biological Databases and online Resource

JVC Eric Bongcam

0930 -1030 Lecture: Overview of Next Generation Sequencing (NGS Technologies)

JVC Walter Verweij

1030 – 1045 Tea Break JVC 1045 – 1300 Lecture: Read quality Assessment & Improvement and

Algorithms behind assembly of short reads and mapping short reads to the genome (Bowtie, BWA) Hands on: Fastqc, Trimmomatic, and Bowtie/Tophat (quality control, assembly, read mapping)

JVC Manpreet Katari

1300 – 1400 Lunch Cafeteria 1400 – 1600 Lecture: Data File Formats

Hands on: Sort, Index, and dedup files in linux Working with the output: introduction to Sam tools , Picard and IGV

JVC Manpreet Katari

1600 - 1615 Tea Break JVC 1615 – 1800 Hands on: Variant calling exercise.

Use samtools pileup / GATK pipeline Filter vcf files View results on IGV

JVC Manpreet Katari

FRIDAY 12 AUGUST

0800 – 0830 Outline of day 5 activities JVC Dedan Githae and Joyce Nzioki 0830 – 1000 Lecture: Transcriptomics (RNA-SEQ) using Next Generation

Sequencing (NGS) Technologies. • Statistical Analysis of RNA-seq data. • Normalizing your data. • Basic Statistics to determine differentially Expressed genes • Correcting for multiple hypothesis testing

JVC Manpreet Katari

1000 – 1015 Tea Break JVC 1015 – 1300 Hands on: Mapping an example dataset to a reference genome

with tophat. • Introduction to Bioconductor. • Differential expression analysis with DESeq • Visualizing the results

JVC Manpreet Katari

1300 – 1400 Lunch Cafeteria 1400 – 1600 Lecture: Making Sense of results: Clustering and GSEA

• Different methods for clustering data • Correlation and clustering of data (looking at heatmaps) • Hypergeometric tests: Go-terms and PFAM enrichment

analysis

JVC Manpreet Katari

1600 - 1615 Tea Break JVC 1615 – 1800 Hands on: Clustering and GSEA analysis

• Hierarchical clustering and heatmaps • GOstats package • Visualizing results

JVC Manpreet Katari

SATURDAY 13 AUGUST 0900 – 0930 Outline of day 6 activities JVC Dedan Githae and Joyce Nzioki 0930 – 1000 Continued Analysis from the above on NGS Data Analysis JVC All Bioinformatics Trainers 1000 – 1015 Tea Break JVC 1015 – 1300 Question and Answer Group Discussion. JVC Lead by Dedan Githae 1300 – 1400 Lunch Cafeteria 1400-1600 FREE AFTERNOON

SUNDAY 14 AUGUST – DAY OF REST

MONDAY 15 AUGUST 0800 – 0830 Outline of day 7 activities JVC Dedan Githae / Joyce Nzioki 0830 – 0900 Introduction to 16S Metagenomics JVC Hadrien Gourlé 0900 – 1100 Laboratory:16S Metagenomics and DNA Quantification Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1100 – 1115 Tea Break JVC 1115 – 1300 Laboratory: V2-V4 16S Region Amplification Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1300 – 1400 Lunch Cafeteria 1400 – 1530 Laboratory: 16S PCR Products agarose gel electrophoresis Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1530 - 1545 Tea Break JVC 1545 – 1800 Laboratory: 16S PCR product purification Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge

TUESDAY 16 AUGUST 0800 – 0830 Outline of day 8 activities JVC Dedan Githae / Joyce Nzioki 0830 – 1100 Laboratory: Amplicons quality check Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1100 – 1115 Tea Break JVC 1115 – 1300 Laboratory: Pooling Amplicons Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1300 – 1400 Lunch Cafeteria 1400 – 1530 Laboratory: Pool quality check Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge 1530 - 1545 Tea Break JVC 1545 – 1800 Laboratory: Demonstration of 16S Miseq sequencing Lab4 Tilly Eldridge, Eunice Machuka, Pauline

Asami, Collins Mutai, Vincent Njunge

WEDNESDAY 17 AUGUST

0800 – 0830 Outline of day 9 activities JVC Dedan Githae / Joyce Nzioki 0830 – 1000 Key Note Speaker II JVC 1000 – 1015 Tea Break JVC 1015 – 1100 Lecture: Introduction to Metagenomics data analysis JVC Hadrien Gourlé 1100 – 1300 Hands-on: Pre-processing your data

Introduction to rRNa databases JVC Hadrien Gourlé

1300 – 1400 Lunch Cafeteria 1400 - 1430 Participants Action Plans (PAPA Tool) JVC Wellington Ekaya 1430 – 1530 Hands-on: Metagenomics data analysis

OUT based analysis JVC Hadrien Gourlé

1530 - 1545 Tea Break JVC 1545 – 1800 Hands-on: Visualisation of the results JVC Hadrien Gourlé

THURSDAY 18 AUGUST 0800 – 0830 Outline of day 10 activities JVC Dedan Githae / Joyce Nzioki 0830 – 1000 Hands-on: Introduction to Whole Metagenome Sequencing

Metagenomic Assembly JVC Hadrien Gourlé

1000 – 1015 Tea Break JVC 1015 – 1300 Hands-on: Comparative Functional Analysis JVC Hadrien Gourlé 1300 – 1400 Lunch Cafeteria 1400 – 1530 LAB TOUR Lab All participants / Julius Osaso 1530 - 1545 Tea Break JVC 1545 – 1800 Lectures: Statistics application to 16S Metagenomics

• Introduction to Principal Component Analysis (PCA) • Introduction to Distance Measures • Introduction to Principal Coordinate Analysis (PcoA) • Introduction to Analysis of Molecular Variance

(AMOVA) • Measure of diversity (Richness, Simpson and Shannon)

JVC Stephen Opiyo

FRIDAY 19 AUGUST 0800 – 0830 Outline of day 11 activities JVC Dedan Githae / Joyce Nzioki 0830 – 1000 Lecture: MSA and Phylogenetics JVC Manpreet Katari 1000 – 1015 Tea Break JVC 1015 – 1245 Hands-on: MSA and Phylogenetics JVC Manpreet Katari 1245 - 1300 Post Workshop Test JVC Dedan Githae/Joyce Njuguna 1300 – 1415 Lunch Cafeteria 1415 - 1500 Feedback / Course Evaluation JVC All participants 1500 – 1600 FINAL SESSION

Workshop closing remarks Award of Certificates

JVC Wellington Ekaya - (Senior Scientist - Capacity Building) Appolinaire Djikeng – Director, BecA-ILRI Hub Trainers

1600 - 1615 Tea Break JVC 1900 – 2100 Dinner All Participants and trainers