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Sathyabama Institute of Science and Technology (SIST), Chennai- 600119.Contact - Dr. Amit Kumar, [email protected]; [email protected]
Introductory Course on nd2 Next Generation Amplicon Sequencing- Data Analysis
Basics of NGS
Data comprehension
University of East Angila,United Kingdom.
Sathyabama Institute of Science & Technology Chennai, India.
Pathfinder Research and Training Foundation, New Delhi, India.
Dr. Kumari Richa, Ph.D.
Dr. Amit Kumar, Ph.D.
Dr. Aditya Arya, Ph.D.
Course Instructors
27 - 29 June 2018
Analysis Hands on
Workshop module series
Next Generation Amplicon SequencingData Analysis
Editors
Dr. Aditya AryaDr. Amit Kumar
Dr. Richa Kumari Dr Vinu SS
Free Booklet worth Rs 400/-
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, NGS methods 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. After a huge success of first training program as two day course, we have developed improved three day program, where participants will learn how to analyze NGS amplicon sequence data from scratch. The training will begin with very basics of NGS technologies followed by extensive 15 hours hands-on sessions that will include all the steps needed to analyze the sequences and interpret data (special focus on amplicon) primarily using Mothur. In addition, a working knowledge and hands on learning will also be provided on Galaxy and Basespace.
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. Prospective participants may span but not remain limited to naive masters students to PhD students, post docs etc. It is expected that all the participants bring their own laptop and charger for convenience as most part of training will be based on live training.
About Instructors
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.
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.
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.
Dr. Kumari Richa
Dr. Amit Kumar
Dr. Aditya Arya
General Information about the course
Where: Sathyabama Institute of Science and Technology
Chennai- 600119, India.
When: 27-29 June 2018.
Who can apply: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.
How to apply:Email your CV and brief purpose to attend to the
organizers. Registration is limited to 30 participants only
What to bring: Participants will need to bring their own laptop.
Benefits of the course:· 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.
Course Coverage Basic introduction: Overview of major NGS platforms
and methods, commonly used tools and examples of datasets Data analysis : 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)
Course FeeM.Sc. and PhD Students - 2500/-, Post-doc - 3500
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.
Deadline: th10 June 2018
Organizer Details: Dr. Amit Kumar, Scientist
Email:[email protected](please write “course on amplicon seq analysis” in the subject line of email)
Address: International Research Centre for Climate Change Studies, Sathyabama Chennai-600119, India.
Phone: +91 9094486533; 9811886440
