Introduction to Next-generation sequencing data analysis with SUSHI

Course Description

This informatics training course provides an introduction to SUSHI, NGS data analysis framework, developed at FGCZ, focusing on typical usecases in genomics (DNA) and transcriptomics (RNA) data analyses. The course also provides the lecture about the key concept of SUSHI framework itself, tips for the reproducible research, and some applications in case of job failure and further data analysis beyond SUSHI workflow.

Learning Objectives

At the end of the course, the participants will
- understand the typical steps and workflows involved in RNAseq and DNA​seq data analysis
- perform workflows associated to the analysis of RNA​seq and DNAseq data with SUSHI
- understand the concepts and mechanisms behind the SUSHI framework
- understand how to use SUSHI for reproducible research

Course Programme

- Introduction to SUSHI and to the general issues in NGS data analysis
- Demonstration and practical of RNA-​/DNA-​seq data analyses in SUSHI
- Lecture about the key concept of reproducible research in NGS data analysis
- Tips on further data analysis beyond the SUSHI workflows
Note
- The course materials in practical are mostly same to the other Bioinformatics courses, so you may feel redundant if you take other courses such as RNAseq, Variant calling courses at FGCZ.
- This course focuses on SUSHI system and usage itself rather than the mathematical/statistical theories behind the NGS data analysis.
- Besides the course, we plan to provide SUSHI monthly seminars (free, online). In this seminar, we introduce SUSHI applications and usage. One session will focus on one SUSHI application or one typical workflow (some seminars are partially duplicated with the SUSHI course contents).
- The contents will be updated and determined:

https://fgcz-intranet.uzh.ch/tiki-index.php?page=SUSHI-go-round

Language

The course will be entirely taught in English

Participants

The course is limited to 12 participants

Target audience and prerequisites

Applicants should be FGCZ users that have NGS data generated or have data generation ongoing at the FGCZ. The practical will be performed using the SUSHI framework, so no pre-​existing knowledge of Unix or command line environment is required. Participants should attend the course onsite at the FGCZ. 

Cost

Internal flat fee of 50 CHF (only ETH and UZH members are eligible to take part in this course).

An invoice will be issued upon registration. This invoice will be sent out by email as well as a hard copy by regular mail/post. Those participants that register will be sent an email reserving their place together with an ‘Application Form’ to be signed by their correspondent supervisor and emailed back to the FGCZ. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed.

Cancellation Policy

Please note that due to the high demand for this course any change related to your participation should be informed as soon as possible, but not later than ten (10) working days prior to the course start date. The notice must be e-mailed to .
If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.

Please do not hesitate to contact us should you need any additional information or encounter any problems.

Expenses

Please beware that travel expenses, accommodation and meals are not included in the Tuition Fee. These will have to be covered by the participant entirely.

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