ProgrammeAdvanced Genomics and Bioinformatics Training Workshop

BecA-ILRI Hub, ILRI Campus, 7th -19th AUGUST 2016

TIME ACTIVITY ROOM RESOURCE PERSONSUNDAY 7 AUGUST

0800 – 0830

Arrival and Registration JVC Joyce NziokiMarvin 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)

(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 AUGUST0800 – 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 Njunge1530 - 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 AUGUST0800 – 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

JVCStephen Opiyo

1100 – 1115

Tea Break JVC

1115 – 1300

Introduction to Statistics: Descriptive statistics Hypothesis testing Parametric statistics (T-Test and ANOVA)

JVCStephen Opiyo

1300 – 1400

Lunch Cafeteria

1400 – 1530

Introduction to Statistics: Non-parametric statistics (Mann-Whitney U test

and Kruskal-Wallis) Correlations

JVCStephen Opiyo

1530 - 1545

Tea Break JVC

1545 – 1800

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

JVC

Stephen OpiyoWENESDAY 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 AUGUST0800 – 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 FormatsHands on: Sort, Index, and dedup files in linuxWorking 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 pipelineFilter vcf filesView results on IGV

JVC Manpreet Katari

FRIDAY 12 AUGUST0800 – 0830

Outline of day 5 activities JVC Dedan Githae and Joyce Nzioki

0830 – 1000

Lecture: Transcriptomics (RNA-SEQ) using Next JVC Manpreet Katari

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

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 AUGUST0900 – 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 AFTERNOONSUNDAY 14 AUGUST – DAY OF REST

MONDAY 15 AUGUST0800 – 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 – Lunch Cafeter

1400 ia1400 – 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 AUGUST0800 – 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 – Laboratory: Demonstration of 16S Miseq sequencing Lab4 Tilly Eldridge, Eunice Machuka,

1800 Pauline Asami, Collins Mutai, Vincent Njunge

WENESDAY 17 AUGUST0800 – 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 AUGUST0800 – 0830

Outline of day 10 activities JVC Dedan Githae / Joyce Nzioki

0830 – Hands-on: Introduction to Whole Metagenome JVC Hadrien Gourlé

1000 Sequencing Metagenomic Assembly

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 AUGUST0800 – 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 SESSIONWorkshop closing remarksAward of Certificates

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

1600 - 1615

Tea Break JVC

1900 – 2100

Dinner All Participants and trainers