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 essentials
  
• RNA sequence analysis workflow essentials
  

AUDIENCE

This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. We currently do not accept international applicants due to high volume of applicants.

DATES

Workshop dates: 13-Nov-2023 - 17-Nov-2023
Application opens:  07-Jun-2023
Application closes: 03-Oct-2023
Confirmation of acceptance:  Week 41, 2023

LOCATION

E10: 1309 Links to an external site.,
Entrance C11,
Biomedical Centre (BMC) / SciLifeLab
Uppsala University
Husargatan 3,
752 37 Uppsala

FEE

The fee for this on-site workshop is 3000 SEK payed by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. 

Note that travel and accommodation is not included in the fee and must be arranged by the participants. 

CREDITS & CERTIFICATE

Please note that NBIS training events do not provide any formal university credits. 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. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop.

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.
• Demonstrate hands-on experience with handling raw RNA sequencing data, QC and quantification of gene expression.
• Explain the steps involved in differential gene expression using RNA seq data.

ENTRY REQUIREMENTS

• BYOL, bring your own laptop configured according to precourse instructions.
• A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.

• Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.

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.

2023 | National Bioinformatics Infrastructure Sweden