Submission Procedure

Ridom SeqSphere+ allows to submit raw read data (FASTQ) together with epidemiological data of a Sample to the European Nucleotide Archive (ENA).

Important: This function can only be used to submit new ENA entries, and not to update existing once. If a Sample is submitted a second time to the same study, the submission will fail.

As for all public submission in SeqSphere+ the Submission Anonymization Filter is shown as first step. In the next step the raw reads are selected for the submission. If the Sample was created from raw reads in pipeline mode, the FASTQs files are associated to the Sample and are automatically filled in and the dialog can be confirmed.

Next the submission dialog window opens, and shows the ENA account specifications and the submission data for each Sample. Mandatory fields are marked by *.

The ENA Account specifications consists of

• Center name
• Login
• Password
• Study accession number
• Transfer protocol

The first 3 values are stored per SeqSphere+ user in the database and can be edited with the menu item Options | User Settings. The study accession number must be entered manually for each submission. The study must already be existing. New studies and accounts can be created manually at ENA Webin. The transfer protocol default value is FTP which can be changed to FASP (Aspera) as described below in IBM Aspera section.

Initial editor values are taken from the Sample's data fields and from the Procedure Details, anonymized according to the settings in the Submission Anonymization Filter. The Copy values to other editors button can be used to copy data from the editor in the currently selected tab to all other editors. Make sure the box next to "I ensure that the data submitted is ..." is selected, then click OK to start the submission to ENA.

If the Samples use a Database Scheme that contains the field EBI/NCBI Accession(s), the ENA run accession numbers are appended to this field.

Hint: A Source Type other than "unknown" must be given if a value for Isolation Source is specified. If Source Type is "clinical/host-associated" a value for Host must be given. Host, Host Age, Host Sex, and Host Disease can only be submitted if Source Type is "clinical/host-associated" and a Host is given. Host Disease is submitted as "host_disease_stage" if it is "healthy". Other values are ignored and not submitted.

Warning: Make sure the entered data is correct because it might be difficult or impossible to remove the data from ENA once a Sample is submitted! In any case removal of data from ENA is not possible with SeqSphere+ and requires an interaction with EBI ENA curators.

Genus and Species

Although genus and species are no mandatory fields, they are required to find a Taxon ID from NCBI Taxonomy. Genus and species are concatenated and sent to the NCBI server. The returned Taxon ID is mandatory for ENA submission. If no Taxon ID can be found an error message is generated. If genus and species information is not available, please enter "unknown" in both input fields. This will result in Taxon ID 32644, "unidentified".

IBM Aspera

SeqSphere+ users can perform alternatively the submission to ENA by using IBM Aspera (FASP) which is faster than standard FTP. In addition, it provides a comprehensive built-in security model and data encryption that does not effect its significant transfer speed. Aspera is using a different port than FTP (default 33001).

Aspera is not deployed with SeqSphere+. For using this feature users have to install a version of the IBM Aspera Desktop Client.

Installing the IBM Aspera Desktop Client

Installation on Windows

The Aspera Desktop Client can be found through IBM Aspera Downloads. By selecting the Windows icon and choosing the latest available version a Download button will appear. By pressing this Download button the user can download the executable file. After the download has finished the user can install the application (Administrator privilege is required).

Through installation steps an Username and a Password must be defined in the IBM Service Account dialog. The username and password are arbitrary and could be used for other Aspera Desktop Client functionalities which are NOT related to SeqSphere+. More information regarding the installation steps can be found in Aspera Client Documentation for Windows. After the installation of Aspera the SeqSphere+ client must be restarted for this change to take effect.

Installation on Linux (Ubuntu 1804)

The Aspera Desktop Client can be found through IBM Aspera Downloads. By selecting Linux Deb and choosing the latest available version a Download button will appear and also an application user guide is presented in different formats. By pressing this Download button the user can download the Debian Software Package file. To proceed with the installation through the terminal the following command can be used:

$ sudo apt-get install /path_to_installer/aspera-desktopclient-version.deb

More information regarding the installation commands for other Linux distributions can be found in Aspera Client Documentation for Linux. After the installation of Aspera the SeqSphere+ client must be restarted for this change to take effect.

Enabling Aspera in SeqSphere+

The Transfer protocol can be selected in the last dialog of the ENA submission procedure. By default only FTP is available in this field. If the Aspera Desktop Client was installed, FASP (Aspera) can be chosen in addition here to use the Aspera client for ENA submissions.