Certificate Course on Next Generation Sequencing Data Analysis
Date: 06th - 09th October 2015 and 10th – 13th October, 2015
Time: 9:00 am to 5:00 pm all days
Venue: Bioinformatics Lab 2
Coordinator: Mr. Naveen P
Objectives of the Workshop
Next Generation Sequencing (NGS) has revolutionized the way we carry out biological research today. Various NGS platforms in the market such as Illumina, SOLiD, and Roche, offer unprecedented ability to apply massively parallel sequencing of transcriptomic (RNA) and genomic (DNA) samples to understand disease and health. The enormous data pose a fundamental problem of management and analysis. This workshop aims at introducing the various platforms of Next Generation Sequencing and data analysis solutions that eliminates the next-generation DNA sequencing data management and provide advanced next-generation bioinformatics visualization capabilities. The workshop integrates cutting-edge bioinformatics algorithms with high-performance computing solutions to empower graduate and post graduate students of the D.Y Patil University School of Biotechnology and Bioinformatics to seamlessly sail through the data deluge enabling them to focus on research questions.
The sessions were organized by IBioA, Ahmedabad. The hands on session were carried out by remote accessing their servers.
The sessions were carried out by experts from IBioA Ahmedabad.
Dr. Rohan Machar, Dr. Senthil, Dr. Vivel Tanavde, Mr. Pinal
Workshop Details
30 students benefitted from 2 sessions of the workshop. All the sessions were very well planned. The speakers started with the basics and explained all the concepts very clearly. The server located in IBioA Ahmedabad was remote accessed and hands-on session was carried out. As the students were from a mixed group of Under Graduate and Post Graduate, the interactions were very live and problems were solved with real enthusiasm.
The course was designed by IBioA and C-CAMP (Center for Cellular and Molecular Platforms) Bangalore. All the students were tested with an objective answer question paper for 40 marks at the end of the fourth day and certificates were issued.
Time | Duration | Event | |
Day 1 | |||
10:00 – 11.00 | 1hr | Introduction to Genomics field | |
11:00 – 12:30 | 1 ½ hr | Sequencing Technologies: Sanger and Next Generation Sequencing (NGS), applications and challenges | |
12:30 – 1:00 | ½ hr | Linux Introduction Talk and Demo | |
1:00 – 1:30 | 1 hr | Lunch break | |
1:30 – 2:30 | 1 hr | Practical: Linux operating system | |
2:30 – 3:30 | 1 | Lecture and Demo: NGS file formats and quality filtering of NGS data using NGSQC Toolkit | |
3:30 – 4:00 | ½ hr | Tea break | |
4:00 – 5:00 | 1 hr | Practical: Quality filtering with NGS QC Toolkit | |
Day 2 | |||
10:00 – 11.00 | 1hr | Role of Genomics on modern medicine, agriculture and biotechnology | |
11:00 – 12:30 | 1 ½ hr | Introduction to Whole Genome Sequencing in prokaryotes andEukaryotes and challenges | |
12:30 – 1:30 | 1hr | Lunch | |
1:30 – 2:30 | ½ hr | Demo : De novo assembly and Reference based assembly of whole genome | |
2:30 – 3:30 | 1 hr | Practical De novo assembly with Minia | |
3:30 – 4:00 | 1 hr | Tea break | |
4:00 – 5:00 | ½ hr | Practical: Reference based assembly with BWA | |
Day 3 | |||
10:00 – 11.00 | 1 hr | SNP and Pharmacogenomics | |
11:00 – 12:00 | 1 hr | Introduction to Epigenome: Methylation & Acetylation | |
12:00 – 1:00 | 1 hr | Lecture: Introduction to RNA-seq and dealing with RNA Seq Data | |
1:00 – 1:30 | ½ hr | Lunch break | |
1:30 – 2:30 | 1 hr | Demo: Dealing with RNA Seq Data with TopHat and Cufflinks | |
2:30 – 3:30 | 1 hr | Practical : RNA-Seq Analysis TopHat | |
3:30 – 4:00 | ½ hr | Tea break | |
4:00 – 5:00 | 1 hr | Practical: RNA-Seq Analysis Cufflinks | |
Day 4 | |||
10:00 – 11.00 | 1hr | Genome wide association studies in disease.What is GWAS, How to design a GWAS study, what information can it yield. | |
11:00 – 12:00 | 1hr | Introduction to Metagenomics, challenges and current research | |
12:00 – 1:00 | 1hr | Talk: Dealing with Metagenomics data with MGRAST | |
1:00 – 1:30 | ½ hr | Lunch break | |
1:30 – 2:30 | 1 hr | Demo: Dealing with Metagenomics data with MGRAST | |
2:30 – 3:30 | 1 hr | Practical : Metagenomics Analysis MGRAST | |
3:30 – 4:00 | ½ hr | Tea break | |
4:00 – 5:00 | 1 hr | Faculties-student discussion, assessment and certificate distribution |