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

25-Nov-2024 - 29-Nov-2024

Linköping

This training event has a fee of 3000SEK for applicants affiliated to academia. Fee for applicants from industry is 15000SEK. If you accept a position at the workshop and do not participate (no-show) you will still be invoiced. Please note that NBIS cannot invoice individuals, so we will need an institution billing reference for registration.

INFO

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

This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare.

Required to be able to follow the tutorials:

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

To get the maximum benefit from the workshop:

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

The course can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. 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 other researchers. International applicants are accepted based on availability of seats

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.

REGISTRATION

Application form: https://nbis.typeform.com/to/dSKKEqMZ
Application opens: 08-June-2024
Application closes: 13-Oct-2024
Confirmation of acceptance: About 1 week after application closes

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.

2024 | National Bioinformatics Infrastructure Sweden