th st30 - 31 August 2017

International Research Centre, Sathyabama University, Chennai- 600119

Next Generation Amplicon Sequencing-

Data Analysis

Introductory Course on

First

Kumari Richa, Ph.D.

Amit Kumar, Ph.D.

Aditya Arya, PhD

Stazione Zoologica Anton Dohrn, Naples, Italy

Sathyabama University, Chennai, India

Pathfinder Research and Training Foundation, Delhi India

Instructors

About the program

The advent of next generation sequencing (NGS) technologies such as Illumina and ion torrent has emerged as a breakthrough in the field of molecular microbial ecology. These technologies provide a more comprehensive picture of bacterial community diversity due relatively much higher sequencing depth. Alongside due to their reduced cost per base sequencing, they are more economical, hence the preferred choice. However, the bioinformatics needed to analyze the sequence data generated by the NGS techniques is challenging for students and early career researchers who are biologists. They often need training to begin processing of the sequence and to decide what tools (e.g. statistical) they need for better and correct interpretation of their data. During this two day course, participants will learn how to analyze NGS amplicon sequence data from scratch. We will cover a brief theoretical aspect of SSU ribosomal gene amplicon sequencing followed by extensive 15 hours hands-on sessions that will include all the steps needed to analyze the sequences and interpret data on microbial diversity and their community structure. We will provide a real NGS data (Illumina) of 16S amplicons, which we will together use to perform the raw sequence analysis, statistical analysis and data interpretation.

Participants do not need to have any prior experience with NGS data analysis, however, basics of molecular biology and strong motivation to undergo extensive training is highly desirable.

About Instructors

Dr. Kumari Richa

Kumari Richa has been extensively working on molecular microbial ecology for past 5 years. She has extensively studied the microbial communities of various marine habitats using high-throughput sequencing (Illumina) of SSU rRNA gene amplicons, flow cytometry and MAR-CARD-FISH.

Dr. Amit Kumar Amit Kumar has been working on marine molecular diversity of both prokaryotic and eukaryotic fraction of microbial communities for past 7 years. Besides, he is also engaged in investigating molecular response of marine organisms using Illumina based RNA-Sequencing.

Dr. Aditya Arya

Aditya Arya has been working on the novel antioxidant mimetic nanomaterials especilally their biological impact and effects at sub-cellular and physiological level. His work involved a number of systems biology related approaches to demostrate the metabolic effects of nanoparticles. He has been trained at many prestigious institutes such as Sanger Institute (Cambridge), EMBL (Heidelberg) etc.

General Information about the course

Organizer Details:

Where:

When:

Who can apply:

How to apply:

What to bring:

Benefits of the course:

Topics to be covered:

Costs: 2000/- INR only.

Deadline:

Innternational Research Centre, Sathyabama University, Chennai- 600119, India.

30-31 August 2017.

Graduate students, postdoctoral scholars, and any researcher using or aim to use amplicon sequencing in the field of

environmental microbiology, evolutionary biology, or any other related field.

Email your CV and brief purpose to attend to the organizers. Registration is limited to 20 participants only

Participants will need to bring their own laptop.

· Hands-on training on real NGS data from raw analysis to statistics and result interpretation

· Practical understanding of various softwares/tools involved in the NGS amplicon sequence analysis

· Basic terminologies and concepts of the microbial ecology · Interaction with instructors for questions on your own dataset.

Theoretical concept: Introduction to the global use of SSU rRNA gene/ rRNA for investigating microbial diversity, community

composition and activity. Practical: Quality control of sequence

data, pre-processing of data to obtain high-quality reads, alignment with reference databases, chimera removal, clustering,

classification, OTU based analysis: Rarefaction, α- and β-diversity estimation, general statistical analysis: Correlation, PCA, T-test; Multivariate statistical analysis, building phylogenetic tree using

NGS data, Unifrac (Detailed program to be communicate after selection of participants)

The cost includes accommodation at the University hostel, study

materials, and training manual. Participants are required to arrange their own travel to the site Registration fee

should be paid through demand draft in favor of “Dean (Publications & Conferences) Sathyabama University”

Payable at Chennai. or

Through Online transfer A/c No. 891734627, Indian Bank

IFSC: IDIB 000T0 20.

th20 August 2017

Dr. Amit Kumar and Dr. Vinu SivaEmail: amit.kumar.szn@gmail.com; vinusiva@gmail.com

(please write “course on amplicon seq analysis” in the subject line of email)

Address: International Research Centre for Climate Change Studies, Sathyabama University, Rajiv Gandhi Salai,

Chennai-600119, India

Phone: +91 9094486533; 9751926980