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Full-day Tutorial
Essential Elements for Next Generation Sequencing Data Analysis

Mode: Onsite

Abstract for Tutorial: With the advent of next-generation sequencing (NGS) technologies, there arose a need to identify candidate mutations for causality. A challenge often faced in identifying and inferring the causal SNPs from sequence data is that different methods need to be preferentially used to predict the effect of mutations for determining bona fidelity. While there are approaches focused on a wide array of highly sensitive, if not less stringent methods that the NGS has delivered in the recent past, this workshop aims to bridge the gap in using systems genomic approach taking command line scripts to Galaxy based workflows. A special focus of this workshop is on the current trends in genome analyses with special insights into NGS analysis. The sessions largely focus on whole exome sequencing (WES) and whole transcriptome shotgun sequencing (WTSS) or RNA-seq pipelines, and galaxy integrated workflows, latest trends on single cell sequencing with vivid demonstration of various steps of data analysis including quality control and generation of variant calls, gene expression. An ample time will be set aside for discussing case studies on various diseased phenotypes.

Learning Objectives for Tutorial: By the end of the tutorial, the participants shall be able to run WES/RNA-Seq pipelines, identify key themes from the course curriculum based case studies besides differentiating results from each others’ exercises. The tutorial will be interactive with problem oriented questions. The participants are welcome to bring their own datasets in the form of raw reads (fastq). However please limit the total file collection you bring to no more than 20 files, the purpose of the tutorial is to provide the skills for whole cohort analysis, not to complete the end-to-end analysis.

Maximum number of attendees participating: 60

Draft Schedule of the tutorial including coffee breaks (full-day schedule)

  • 10:00-11:00: Introduction to Biology of systems and Q and A.
  • 11:00 -12:00: Systems Genomics in the age of next generation sequencing (NGS)
  • 12:00-12:30: Advances in NGS
  • 12:30-13:00: Teasers and hands-on bash liners
  • 13:00-1400: Lunch
  • 14:00-15:15: Automated galaxy workflows for NGS - Part I
  • 15:15-15:30 hrs: Coffee break
  • 15:30-16:45: Hands-on NGS pipelines; Analyse results –
  • 16:45-17:15 hrs: case studies, automated galaxy workflows a bioinformatics cloud platform for NGS - Part II
  • 17:15-17:30 hrs: Wrap-up and Q and A

Identify and highlight blocks of hands-on content in your submission: As it is all run through linux servers, The organzers are requested to provide a minimum 1 TB RAM/64 processors/50 TB SATA HDD space/Ubuntu make/ for ensuring the participants login through ssh. A few days before the workshop, we will checkmark and benchmark our tools on the server. If in any case, it is not provided, we also have remote access to our participants from our own servers, but we may have to comply with security/firewall issues, if any. Galaxy, however, will be through cloud and all users are requested to have an account at usegalaxy.org. Galaxy based analysis will make use of the Galaxy Training Network (https://training.galaxyproject.org/) as the content is supported on usegalaxy.org. Users intending to make use of Galaxy will be instructed to have already uploaded their data prior to the date of the tutorial. A handbook would be made available to the participants

Tutorial Speakers with titles and affiliations:

Prashanth N Suravajhala, Ph.D. (Prash), Principal Scientist, Amrita University, Kerala, India and Founder, Bioclues.org, India.

A PhD in Systems Biology from Aalborg University, Denmark., Prash went on to gain more than 7 years of postdoctoral experience across four different laboratories. Prash worked for Birla Institute of Scientific Research, Jaipur on his return to India in 2016 where he successfully led three projects in the areas of systems genomics of rare diseases and next generation sequencing analysis of cancers and diabetes. He has interests exploring the known unknown regions in the human genome, primarily working on the top-down systems biology approaches of hypothetical proteins. Over the last 10 years, he has developed an interest in long noncoding RNAs in humans, elucidating the mechanisms underpinning small molecular interactions through clinical exomes. His group has benchmarked pipelines and developed methods for systems genomic integration. He is an Associate Editor of Frontiers in Genetics/Systems Biology, Bio-Protocol, Biomolecules. BMC Medical Genomics to mention a few. Prash is a founder of Bioclues.org, India’s largest bioinformatics society, an affiliate of ISCB. He strongly advocates open access and open science. His group page can be reached at http://www.bioinformatics.org/wiki/Prash

Intended audience and level: The tutorial is intended for all biologists with a flair for bioinformatics, linux command line interface. The participants who do not have an a priori experience of linux commands will be allowed to acclimatise fast with precomputed scripts made available. The Galaxy framework will ease participants who are not familiar with linux command line interface. The tutorial is open for all those semi-experienced or experienced researchers who want to analyse their own data using NGS pipelines.