Hello, your Galaxy SARS2CoV-2 Sequence container is running!

This container is optimized to clean human reads from raw reads, make assemblies and to upload both the assembly and raw reads to ENA, this in only a few steps. The ENA uploading is based on the tool ena-upload-cli while the reads cleaning tool is based on Metagen-FastQC workflow.

ENA submission quick-start

Note: For more detailed information on the container and the ENA submission process read the documentation found on ELIXIR Belgium’s RDM Guide

1. Log in to Galaxy and load your ENA credentials:

Login to Galaxy using admin as username and password as password. This will give you full access to the galaxy instance.
Go to User > Preferences in the top navigation
Click on Manage Information
Fill in the Your ENA Webin account details (If you do not have one, get your ENA Webin account here)
Click Save

2. Upload Data

Upload your raw data using Galaxy’s upload tool found at the top right of the Tools panel or using Upload File from your computer under Upload Data tool group.

3. Filter human reads out of the raw reads

Filter human traces from your raw data using Clean human reads from raw data from the Preprocessing Tools on the left panel.

Select human h38 reference genome
Choose single or paired-end
Select the files to clean
Click on ‘Execute’

4. Upload metadata and submit to ENA

The ENA Upload tool under Submission tools is used to generate the metadata in the right format, associate it with the sequence data files and submit everything to ENA. It is advisable to first test your submissions using the Webin test service where changes are not permanent and are erased every 24 hours.

The tool offers three ways of entering metadata for submission:

Complete the metadata spreadsheet template and upload it as in step 2 or;
Interactively generate the metadata structure or;
Complete the 4 tsv templates and upload as in step 2.

After uploading or completing the metadata, select the corresponding (human traces removed) data files, fill in your affiliation and click on ‘Execute’.

5. Check for a valid submission

Visit Webin online to check on your submissions or dev Webin to check on test submissions. If everything looks fine, publish the data by changing the “Release Date” of the study to a day later than the current day. It can take several days for ENA to index the data and to let it appear in a correct manner. Covid-19 data will also be indexed by the COVID-19 Data Portal

6. Run the variation analysis workflow

There are currently four workflows for variation analysis that cater for different libraries/platform combinations:

Illumina whole genome sequencing (WGS) paired-end (PE) or single-end (SE)
Illumina amplicon (ARCTIC protocol) paired-end
Oxford Nanopore amplicon (ARCTIC protocol)

Go to the workflow section and select the variation analysis workflow suited for your data by clicking on . This brings up the workflow menu.

7. Run the consensus construction workflow

Go to the workflow section and select the Consensus Construction workflow. This workflow takes as input a Variant Call File (vcf) collection (Fig. 8a), an alignment file (bam) collection and SARS-CoV-2 reference genome. Select the appropriate collections and files and Run Workflow. This workflow outputs a consensus sequence collection as well as one multisample fasta with all the consensus sequences.

8. Submit consensus sequence to ENA

Open the consensus sequence submission tool This tool requires a fasta file (single submission) or a multi-fasta file (multiple submissions) as well as the associated metadata.

Visit Webin online to check on your submissions or dev Webin to check on test submissions as explained in section 6