Certificate Course on Next Generation Sequencing Data Analysis

NGS file1
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.




Day 1
10:00 – 11.001hrIntroduction to Genomics field
11:00 – 12:301 ½  hrSequencing Technologies: Sanger and Next Generation Sequencing (NGS), applications and challenges
12:30 – 1:00½ hrLinux Introduction Talk and Demo
1:00 – 1:301 hrLunch break
1:30 – 2:301 hrPractical: Linux operating system
2:30 – 3:301Lecture and Demo: NGS file formats and quality filtering of NGS data using NGSQC Toolkit
3:30 – 4:00½ hrTea break
4:00 – 5:001 hrPractical:  Quality filtering with NGS QC Toolkit
Day 2
10:00 – 11.001hrRole of Genomics on modern medicine, agriculture and biotechnology
11:00 – 12:301 ½  hrIntroduction to Whole Genome Sequencing in prokaryotes andEukaryotes and challenges
12:30 – 1:301hrLunch
1:30 – 2:30½ hrDemo : De novo assembly and Reference based assembly of whole genome
2:30 – 3:301 hrPractical De novo assembly with Minia
3:30 – 4:001 hrTea break
4:00 – 5:00½ hrPractical: Reference based assembly with BWA
Day 3
10:00 – 11.001 hrSNP and Pharmacogenomics
11:00 – 12:001 hrIntroduction to Epigenome: Methylation & Acetylation
12:00 – 1:001 hrLecture: Introduction to RNA-seq and dealing with RNA Seq Data
1:00 – 1:30½ hrLunch break
1:30 – 2:301 hrDemo: Dealing with RNA Seq Data with TopHat and Cufflinks
2:30 – 3:301 hrPractical :  RNA-Seq Analysis TopHat
3:30 – 4:00 ½ hrTea break
4:00 – 5:001 hrPractical: RNA-Seq Analysis Cufflinks
Day 4
10:00 – 11.001hrGenome wide association studies in disease.What is GWAS, How to design a GWAS study, what information can it yield.
11:00 – 12:001hrIntroduction to Metagenomics, challenges and current research
12:00 – 1:001hrTalk: Dealing with Metagenomics data with MGRAST
1:00 – 1:30½ hrLunch break
1:30 – 2:301 hrDemo: Dealing with Metagenomics data with MGRAST
2:30 – 3:301 hrPractical :  Metagenomics Analysis MGRAST
3:30 – 4:00 ½ hrTea break
4:00 – 5:001 hrFaculties-student discussion, assessment and certificate distribution


The students were updated with the latest technologies in Bioinformatics used in Genome analysis. They understood the potential of this field and requested for conduction of advanced courses in NGS Data analysis.