EMBL-EBI Workshop: Analysis of genome scale data from bulk and single-cell sequencing


 Monday 19 Friday 23 November 2018


NIBMG - National Institute of Biomedical Genomics University Of Kalyani,  Kalyani,  West Bengal,  741251,  India

Application opens: 

Thursday 12 July 2018

Application deadline: 

Monday 15 October 2018


Open application with selection


Partha P. Majumder

Registration fee: 


Registration closed

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Course Overview

This course will provide practical training to researchers in India who are engaged in research or applications that involve analyses of data generated by massively-parallel DNA sequencers using DNA isolated from bulk cells or a single-cell. This course will provide an introduction to the technology, data analysis, and key bioinformatics tools and databases. The content is intended to provide a broad overview of the subject areas, and to highlight key resources, approaches and methodologies. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets and there will not be scope to analyse personal data.


This course is open to all scientists and application specialists who are engaged in genome-scale research. Preference will be given to junior-level scientists who can in turn train others in their institutions.

No knowledge of programming is required, but an undergraduate level knowledge of biology is required.


  • ensemblensembl-genomes
  • expression-atlas-gene-expression-across-species-and-biological-conditions

Learning outcomes

After this course you should be able to:

  • Use basic statistics, UNIX and R commands to navigate the command line, employ and interpret statistics from NGS data.
  • Use a range of bioinformatics software and tools to undertake basic analysis of NGS data
  • State the advantages and limitations of NGS analyses
  • Apply various CNV detection methods
  • Submit, browse and access a range of NGS data available in public repositories using EBI resources


Day 1 – Monday 19 November
08:30 - 08:40 Welcome Partha Majumder
08:40 - 09:35 Introductions and networking Cath Brooksbank
09:35 - 09:45 Gratitude Partha Majumder
09:45-10:00 Break  
10:00-11:00 Statistics: Probability, Distributions, Tests of significance Partha Majumder
11:00-13:00 Overview of NGS Technologies: Platforms, Chemistry, library preparation Arindam Maitra
13:00-14:00 Lunch
14:00-15:30 Introduction to EMBL-EBI Resources Cath Brooksbank, Astrid Gall, Laura Huerta
15:30-17:00 Introduction to ENA and NGS Workflows Sam Holt (webinar)
17:00-17:30 Break  
17:30-19:30 Introduction to Ensembl Astrid Gall
19:30 End of Day 1  
Day 2 – Tuesday 20 November
08:30-10:15 Introduction to NGS Data Analysis Nidhan Biswas
10:15-10:30 Break  
10:30-12:30 Linux: Introduction to the Command Line Nidhan Biswas
12:30-13:30 Lunch  
13:30-15:00 Introduction to NGS file formats, databases and associated tools Chitrarpita Das
15:00-15:30 NGS Data QC Swati Jaiswal
15:30-16:30 Exome Sequence data analysis: Alignment, Read Filtering, Variant Calling Nidhan Biswas
16:30-17:00 Variant annotation and Variant Filtration Nidhan Biswas
17:00-17:15 Break  
17:15-18:15 Introduction to R: Commands & Functions Saroj Mohapatra
18:15-19:00 Case Study: Data Processing through R Saroj Mohapatra
19:00 End of Day 2  
Day 3 – Wednesday 21 November
08:30-09:30 Read and Mutation Visualization through IGV Arnab Ghosh
09:30-10:30 Read Visualization in Ensembl Astrid Gall
10:30-10:45 Break  
10:45-11:30 Analysis of Genome Structural Alterations: CNV & SV Chitrarpati Das
11:30-12:30 CNV Detection from Genome-WIde Array Data Nidhan Biswas & Chitrarpati Das
12:30-13:00 CNV Detection from Sequence Data: Paired-end and Mate-pair Nidhan Biswas & Chitrapati Das
13:00-14:00 Lunch  
14:00-16:00 Ensembl workshop - Variation / VEP Astrid Gall
16:00-16:30 Introduction to DGVa for CNV Data Baron Koylass (webinar)
16:30-17:00 Break  
17:00-18:30 Ensembl workshop - Regulation Astrid Gall
19:00 Special dinner  
Day 4 – Thursday 22 November
08:30-09:30 Ensembl workshop - Comparative Genomics Astrid Gall
09:30-10:30 Ensembl workshop - Biomart (Data export tool) Astrid Gall
10:30-10:45 Break  
10:45-11:15 Targeted Sequencing and its application Arindam Maitra
11:15-11:45 RNA-Seq: libraries to data generation Arindam Maitra
11:45-13:00 Bulk RNA sequencing Analabha Basu
13:00-14:00 Lunch  
14:00-15:45 Bulk RNA sequencing practical Debodipta Das & Shatakshee Chatterjee
15:45-16:45 Circos - Mutation and CNV Visualization Arnab Ghosh
16:45-17:00 Break  
17:00-18:00 Introduction to EVA Baron Koylass (webinar)
18:00-19:00 COSMIC data resource for cancer mutations Simon Forbes & Nidhi Bindal(webinar)
19:00 End of day 4  
Day 5 – Friday 23 November
08:30-10:30 Transcriptomic data resources and tools Laura Huerta
10:30-11:00 Break  
11:00-12:30 Transcriptomic data resources and tools Laura Huerta
12:30-13:30 Lunch  
13:30-14:30 Single-cell RNA sequencing and the Human Cell Atlas Laura Huerta & Dani Welter (webinar)
14:30-16:00 Single cell RNA sequencing: Methods Arindam Maitra
16:00-17:00 Single cell RNA sequencing: Analysis approaches and considerations Nidhan Biswas
17:00-17:15 Break  
17:15-17:45 Data integration challenges and solutions Partha Majumder
17:45-18:00 Wrap-up and feedback