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Workshop Registrations Closed

Workshop

We will send you an email with specifics about the workshop by Sep 20th. However, for planning purposes, please find below the details for your reference:
  • The workshop is a residential program. All participants are expected to stay at the CCMB guest house. Housing is double occupancy. The workshop fee is inclusive of the housing and food.
  • If you are participating in Part II (Sep 24th-27th) or Part 1 and 2 of the workshop (Sep 24th to Sep 30th) you can check in at the guest house on Oct 23rd PM - details will be sent
  • Part I of the workshop will start on Sep 24th at 9:00am and end on Sep 27th by 2:00pm
  • Part II of the workshop will start on Sep 27th at 11:00am and end on Sep 30th by 7:00pm
  • Pre-requisite workshop material will be posted and a link will be sent by Sep 20th

Hands on NGS Wetlab (Part I) - Sep 24th (Thursday) – Sep 27th (Sunday) Limited to 20 students and will work as a pair during the hands on session

Sep 24th, 2015
9:00 am - Registration check-in 9:00am
10:00am NGS technology overview
11:00am - 6pm – Library prep
  • Nextera library prep (plan to make libraries using large constructs BACs and possibly a bacterial genome.

Sep 25th, 2015
9:00am – 6:00pm Sequencing
  • Quantify pool and Sequence the libraries on Illumina MiSeq
  • If time permits will make another library starting at 9:oo in parallel (eg: 16s for Metagenomics)

Sep 26th, 2015
9:00am – 6:00pm Sequencing data QC, demultiplexing and preilimnary analysis
  • may possibly start a second round of sequencing this day as needed (details to be refined 9-10 days before the
  • discuss other applications and library prep options

Sep 27th, 2015
9:00-12:00 – Hands on part wrap up; Q&A



Bioinformatics Analysis (Part II) – Sep 27th (Sunday) - Sep 30th (Wednesday) Sep 27th, 2015
1:00-6:00 – Analysis overview; tools and technique
  • Analyze sequence data produced in Part I. For participants who did not participate in part I data will be provide for analysis.

Sep 28th, 2015
9:00-6:00
Project planning – coverage size, read length, barcode etc
Exome amd whole genome analysis
copy # analysis

Sep 29th, 2015
9:00-6:00 – RNA-seq; fusion analysis

Sep 29th, 2015
9:00-6:00 – Other advanced data analysis and application

Sep 30th
9:00-6:00 – PacBio Single molecule analysis

For registration, please contact: ngbt2015@sgrf.org.in

Illumina/ second gen sequencing applications and analysis I - Mol. Bio basics refresher, Unix command line refresher, NGS sequencing principles and data types, NGS data QC, data demultiplexing, Whole genome sequence (WGS) analysis, Exome analysis and RNA-Seq analysis

Illumina/ second gen sequencing applications and analysis II - NGS project appraisal and sequencing depth calculation for WGS, exome and RNA-seq, Fusion detection using RNA-seq, Variant calling and annotation, and metagenomics, ChIP-Seq analysis, de novo assembly, integrated proteomics/genomics analysis and other advanced topics will be covered.

Third gen sequencing applications and analysis
PacBio Single molecule sequencing and data analysis - PacBio SMRT sequencing technology has fast emerged as game changers in field of genomics. Today research groups are able to assembly full genome, probe complex regions of genome and identify extremely rare mutation by virtue of unbiased long reads. It is important to understand the unique data structure and data analysis algorithms to make optimal use of PacBio long read technology in research applications. This workshop is an attempt to introduce the attendees to finer details of PacBio sequencing data analysis. During this workshop a number of key application would be discussed followed by demo of various protocols available for analysis. PacBio supplies a suite of bioinformatics tool called SMRT analysis that has a friendly graphical user interface - SMRT portal. We will use SMRT portal to demonstrate various ways to analyses pacbio data.

Venue: CCMB, Hyderbad, India.

Course Director: Dr Thangaraj, Professor, CCMB, India and Dr Eric Stawiski, Sr Computational Biologist, Genentech, USA

Dr. Ramprasad VL, COO, MedGenome Lab, Bangalore India
Dr. Eric Stawiski, Sr Computational Biologist, Genentech Inc., USA
Dr. Ravi Gupta, Sr Bioinformatics Scientist, SciGenom Labs., India
Dr. Harsha Gowda, Sr Scientist, Institute of Bioinformatics, India
Dr. Zora Modrusan, Sr Scientist, Genentech Inc., USA
Dr. Saktivel, Scientist, MedGenome Lab, Bangalore India

Additional faculty will be announced soon

We plan to limit the number of participants to 30 for the workshop

Note: Participants have the option of registering for both parts of the works shop or individually for each part. However, preference will be given to registrants who apply for both days. Applicants will be required to submit a copy of their CV and brief statement (100-200 words) of what they expect to learn from the workshop.

Who should attend the workshop
Individuals holding a postgraduate training (M. Sc./Ph.D.) in molecular biology, bioinformatics or a related discipline and interest in gaining hands on experience with next generation sequencing data generation and data analysis will benefit from the course. Students enrolled in a postgraduate training (M. Sc. / Ph.D.) program who have completed basic molecular biology and have hands on exposure to DNA/Protein sequence data (eg: using clustal W, blast etc) are likely to find the course useful.

Course is tailored to accommodate molecular biologists with minimal bioinformatics knowledge (eg: knowledge of sequence alignment programs like clustal W, blast2seq etc) and also individuals with in-depth bioinformatics expertise interested in analyzing next gen sequence data.

Molecular Biologist seeking to gain next gen sequencing data domain knowledge will benefit from this workshop and they should be able to interact with bioinformaticians analyzing next generation sequencing data to ask the right questions and understand the analyzed data

Individuals with bioinformatics training will besides getting an overview of data generation and type of data obtained from Illumina (and iontorrent) will get a hands-on experience with the laboratory side of the NGS data generation. All participants will gain experience in assessing the sequence data quality and also perform hands on analysis of nextgen data, including variant calling (exome-seq) and RNA-seq. An overview of the programs available for analysis in the public domain will also be provided. Participants will get hands on experience with manipulating sample data and analyzed them. The advance section of the course will provide an opportunity to understand NGS project appraisal, sequencing depth requirement assessments, identify gene fusions using RNA-seq data and understand the issues surrounding variant calling and annotation. They will get an opportunity to do hands on annotation of variant call using various databases. The participants will learn about de novo assembly, metagenomic and chip-seq analysis. Over view on integrated genomics proteomics analysis will also be provided.

Optional pre-workshop session: An optional session prior to the workshop will provide a refresher on the molecular biology basics and cover basic commands need to run programs unix/linux terminal.

Certificate for workshop participation will be provided by Institute of Bioinformatics (http://www.ibioinformatics.org), Bangalore.

Workshop Hosts: SGRF, CCMB and IOB

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