2014 NextGen Genomics & Bioinformatics
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Two day workshop will be conducted on Nov 14th and 15th 10:00 am - 5:00 pm
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.
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: Institute of Bioinformatics campus, Discoverer Building, International Tech Park, Whitefield, Bangalore - 560 066 Karnataka, 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. Chee H Lee, Pacific Biosciences
Mr. Anil K. Madugundu, Graduate Research Fellow, Institute of Bioinformatics, India
We plan to limit the number of participants to 30 for the workshop
Note: Participants have the option of registering for both days or each day individually. However, preference will be given to registrants who apply for both days. Applicants registering for day 2 only are expected to have hands one experience with NGS data analysis and have worked on exome and RNA-seq analysis using command line tools on an Unix or Linux environment.
Individuals holding a postgraduate training (M. Sc./Ph.D.) in molecular biology, bioinformatics or a related discipline and interest in next generation sequencing 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 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.
Hotel Melody Inn (http://melodyinn.in/), Whitefield is about ~3km from IOB/ITPL where the workshop will take place.
We have negotiated a special tariff rate with Melody Inn exclusively for participants of this workshop
Single occupancy: Rs 1100/- per night
Double sharing: Rs 800/- per person per night
Note: Breakfast, dinner and Wi-Fi facility will be complimentary.
Please mention the workshop when you book with Melody Inn when you make your booking. We have 25 rooms blocked and the special rates may not be available once these rooms are booked. So plan appropriately.
Workshop Host by: SGRF and Institute of Bioinformatics, Bangalore