Introduction to Bioinformatics using NGS data

An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI).

Briefly, the workshop covers the followings major topics:

• Working on the UNIX/LINUX command line
• Bioinformatic/NGS data formats and QC
• DNA variant calling workflow
• RNA sequence analysis workflow

AUDIENCE

This is intended for PhD students, post-docs, researchers and other employees in Swedish academia and medicine.

DATES

Workshop dates: 28-Mar-2022 - 01-Apr-2022
Application opens:  10-Jan-2021
Application closes: 27-Feb-2022
Confirmation of acceptance:  02-Mar-2022

LOCATION

Online

FEE

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced a 2000 SEK workshop fee.
Please note that NBIS cannot invoice individuals.

DETAILED SYLLABUS

• Working on the unix/linux command line
  • Command line navigation and related commands: cd, mkdir, rm, rmdir
  • Commonly used linux tools: cp, mv, tar, less, more, head, tail, nano, grep, top, man
  • Wildcards
  • Ownership and permissions
  • Symbolic links
  • Piping commands
• Working on remote computing cluster
  • Logging on to UPPMAX
  • Booking resources
  • Job templates, submission and queues
  • Modules
• Commonly used bioinformatic tools and pipelines
• Working with integrated genome viewer
• Variant-calling workflow
  • Mapping reads to the reference genome
  • Variant detection
  • VCF file format
• RNA-Seq workflow
  • RNA-Seq experimental design and considerations
  • QC, mapping and gene expression counts
  • Differential gene expression analyses

LEARNING OUTCOMES

After this workshop you should be able to:

• Describe the basic principles of next generation sequencing.
• Use the Linux command line interface to manage simple file processing operations, and organize directory structures.
• Connect to and work on a remote high performance compute cluster.
• Apply programs in Linux for analysis of NGS data.
• Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.
• Explain common NGS file formats.
• Interpret quality control of NGS reads.
• Explain the steps involved in variant calling using whole genome sequencing data.
• Independently perform a basic variant calling workflow on example data.
• Explain the steps involved in differential gene expression using RNA seq data.
• Hands-on experience with handling of raw RNA sequencing data, QC and quantification of gene expression.
• Conceptual understanding of differential gene expression analysis.

ENTRY REQUIREMENTS

This is a national course open to PhD students, postdocs, group leaders and core facility staff.

A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to

• Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
• It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by Post-Docs, PIs, Healthcare staff etc. Due to the high volume of applications from Swedish institutions, we currently do not accept international applicants.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

APPLICATION

Application form Links to an external site.

CONTACT

Malin Larsson, Martin Dahlö, Roy Francis
edu.intro-ngs [at] nbis.se

CODE OF CONDUCT

By participating in this workshop, you will be agreeing to the NBIS Code of Conduct.

2022 | National Bioinformatics Infrastructure Sweden