27-31th May 2015 and 3-7th Jun 2015
Room 3.41, Third Floor, Centennial Campus,
The University of Hong Kong, Pokfulam Road, Hong Kong.
This intensive 5-days workshop will train attendees on analyzing short-read sequencing data mainly from Illumina, as well as other next-gen platforms. This is a hands-on course and by the end of the workshop the attendees would gain the ability to analyze their own data. The workshop is based on real collaborative projects from our lab, including the analysis of metagenomic data from human and mice experiments in clinical settings, as well as high throughput next generation sequencing of model species.
The hands-on course includes comprehensive practice in analyses of next generation sequencing data, including metagenome, metatranscriptome, single genome resequencing and transcriptomes using common tools, including BWA, samtools, bedtools, GATK, Velvelt, Meta-velvet, IDBA_ud, Trinity, DeSeq and R, etc. Through the course, the participants will learn to:
1. Organize and process files in Linux environment;
2. Deal with the raw Illumina data with quality evaluation and filtering;
3. Map reads to the reference genomes, call SNPs and predict their phenotype consequence;
4. Assemble single genome, transcriptome or metagenome, and predict gene and function and affiliated pathways;
5. Perform statistical analysis of differential expressed genes, enriched gene categories, network analysis, etc.
PhD students, postdocs, research staff and junior faculty members who are interested in, or already working with, next-generation sequencing data are more than welcome. No programming experience is required, although working experience under Linux command-line environment will be highly beneficial. For applicants that lack this knowledge, we will provide a brief introduction and a warm-up practice.
Dr Jun Li, Systems Biology & Bioinformatics Group, School of Biological Sciences, The University of Hong Kong (CV)
Assoc. Prof. Gianni Panagiotou, Systems Biology & Bioinformatics Group, School of Biological Sciences, The University of Hong Kong (CV)
http://sbb.hku.hk
Wednesday 27th of May - Research Assistant Professor Henry Chi Ming Leung, The University of Hong Kong
Thursday 28th of May - Research Assistant Professor Miaoxin Li, The University of Hong Kong
Friday 29th of May - Assistant Professor Silin Zhong, The Chinese University of Hong Kong
Saturday 30th - Assistant Professor, Haiwei Luo, The Chinese University of Hong Kong
Wednesday 3rd of June - Associate Professor S.M Yiu, The University of Hong Kong
Thursday 4th of June - Professor Edwin Chong Wing Cheung, University of Macau
Friday 5th of June - Associate Professor Henrik Bjorn Nielsen, Technical University of Denmark
Saturday 6th of June - Associate Professor John Junwen Wang, The University of Hong Kong
| Day 1, Wednesday May 27th/Jun 3rd, 2015 | |
|---|---|
| 9:00-10:00 | Welcoming and Participants Introduction |
| 10:00-12:00 | Introduction of the Linux system, operation and the computing environment in this course. Introduction of alignment softwares and hands-on practice on BLAST. |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | Analysing the Genomic Variation of Cell Factories in the Era of "New Biotechnology". |
| 14:00-17:30 | Introduction and hands-on practice on quality evaluation and filtering, genome assembly, gene prediction, functional, pathway annotation, SNP calling and related statistical analysis |
| 17:30-18:00 | Tea/coffee break |
| 18:00-19:00 | NGS Special Seminar--Guest speakers: (1)Research Assistant Professor Henry Chi Ming Leung, The University of Hong Kong. / (2)Associate Professor S.M Yiu, The University of Hong Kong. |
| Day 2, Thursday May 28th/Jun 4th, 2015 | |
| 09:00-12:00 | Metagenome analysis: taxonomy profiling, community diversity calculation, assembly, gene prediction, functional and pathway annotation and analysis; (Part I) |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | The Complex Interplay Between Antibiotics and Resistance Phenotypes in the Human Gut. |
| 14:00-17:30 | Metagenome analysis: taxonomy profiling, community diversity calculation, assembly, gene prediction, functional and pathway annotation and analysis; (Part II) |
| 17:30-18:00 | Tea/coffee break |
| 18:00-19:00 | NGS Special Seminar--Guest speakers: (1)Research Assistant Professor Miaoxin Li, The University of Hong Kong. / (2)Professor Edwin Chong Wing Cheung, University of Macau. |
| Day 3, Friday May 29th/Jun 5th, 2015 | |
| 09:00-12:00 | Transcriptome/metatranscriptome analysis: Mapping, assembling, annotation, differential expression at various levels, functional and pathway enrichment analysis and more; (Part I) |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | A Molecular-Level Landscape of Diet-Gut Interactions: Towards Interventions Targeting Specific Bacterial Genes. |
| 14:00-17:30 | Transcriptome/metatranscriptome analysis: Mapping, assembling, annotation, differential expression at various levels, functional and pathway enrichment analysis and more; (Part II) |
| 17:30-18:00 | Tea/coffee break |
| 18:00-19:00 | NGS Special Seminar--Guest speakers: (1)Assistant Professor Silin Zhong, The Chinese University of Hong Kong. / (2)Associate Professor Henrik Bjorn Nielsen, Technical University of Denmark. |
| Day 4, Saturday May 30th/Jun 6th, 2015 | |
| 09:00-12:00 | Advanced genomic, transcriptomic and metagenomic analysis: co-occurrence, co-expression and phenotyp-genotype correlation analyses; (Part I) |
| 12:00-13:00 | Lunch |
| 13:00-13:30 | Feedback survey |
| 13:30-14:00 | Probiotic Modulated Gut Microbiota Suppresses Hepatocellular Carcinoma Growth in Mice. |
| 14:00-17:30 | Advanced genomic, transcriptomic and metagenomic analysis: co-occurrence, co-expression and phenotyp-genotype correlation analyses; (Part II) |
| 17:30-18:00 | Tea/coffee break |
| 18:00-19:00 | NGS Special Seminar--Guest speakers: (1)Assistant Professor, Haiwei Luo, The Chinese University of Hong Kong. / (2)Associate Professor John Junwen Wang, The University of Hong Kong. |
| Day 5, Sunday May 31th/Jun 7th, 2015 | |
| 9:00-11:00 | Advanced topics in NGS data analysis |
| 11:00-11:30 | Tea/coffee break |
| 12:00-12:30 | Take-home messages |
| 12:30-13:30 | Lunch and closing |
| 13:30- | Open practical session with own data (optional) |