Submitting, Finding and Downloading Raw Sequencing Data with ENA

Overview

Making research data FAIR (Findable, Accessible, Interoperable, Reusable) is an essential step during scientific publication. Raw sequencing data are often part of scientific data associated with publications and need to be FAIR. However, these data sets can be very large and challenging to annotate with metadata. There are several specialized repositories with the purpose to store and share sequence data. Each of these has its own accepted data formats, required metadata and portals. However, there is also a lot of interconnectivity between repositories. In this course, we will give an overview of these repositories and data structures in order to guide you to search and submit your sequence data in the right place. In addition, with practical exercises, you will learn how to use these portals by finding, downloading and submitting large datasets. We will mainly focus on the portals and platforms available for submitting to the European Nucleotide Archive (ENA), but many of the taught concepts can be applied to NCBI and DDBJ.

Audience

This course is addressed to life scientists who work with next generation sequencing data and are interested in using ENA for submitting, finding or downloading FAIR sequencing data.

Learning outcomes

At the end of the course, the participants are expected to:

• Understand the main data structures underlying ENA and the Sequence Read Archive (SRA)
• Find an appropriate portal for submitting and finding the most common data types related to raw NGS data
• Use the web interfaces and command line to find and download raw sequencing data from SRA
• Use the command line or FileZilla to upload files with ftp
• Successfully submit the most common data types to ENA

Prerequisites

Knowledge / competencies

Participants are expected to have basic knowledge on common next generation sequencing data types (e.g. fasta, fastq, bam). Experience with the command line (either UNIX or Windows) is a plus.

Technical

Participants are required to have their own personal computer with FileZilla pre-installed.

Application

The registration fees for academics are 100 CHF and 500 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications close on 15/05/2023 or as soon as the places are filled up. Deadline for free-of-charge cancellation is set to 22/05/2023. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place online.

The course will start at 9:00 and end around 17:00.

More information has been provided to the registered participants on 5 June 2023. If this email did not reach you, please check your SPAM folder, or contact the Training group (email at the bottom).

Additional information

Coordination: Patricia Palagi

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.