ENA Data Deposit

Why Deposit to ENA?

Making your sequencing data public is a requirement for most journals and upholds FAIR principles.

Prerequisites (What do I need?)

Before you start the submission process, ensure you have the following components ready.

  • Webin Account: You need a submission account registered at ENA.
  • FASTQ Files: Your raw sequencing data, compressed (.fastq.gz).
  • FTP Client: A tool like FileZilla is required to transfer your files via FTP.

Data Integrity (MD5 Checksum)

When you upload large sequencing files, it is possible for the data to get corrupted during the transfer. To prevent this, we use MD5 checksums.

Think of an MD5 checksum as a “digital fingerprint” for your file.

md5 checksum Generation for your fastq

cd /path/to/your/desirable/directory
md5sum /mnt/new_home/illumina/nextseq2000/name/of/the/run/V*fastq* | awk '{print $2, $1}' | paste - - > filenames_and_checksums_date.txt

FTP Client to ENA

Establish connection. Drag ‘n’ Drop fastq files.

Webin Submission Portal

https://www.ebi.ac.uk/ena/submit/webin/login

Use credentials to login. Navigate to tabs “Submit Reads” and “Register Samples”

The Manifest File

The first component of a successful submission is the Manifest file. This text file tells ENA exactly what your data is. It is submitted via the “Submit Reads” option. Create a file named manifest.tsv or download the spreadsheet template from Webin Submission Portal. For submitting paired reads using fastq files it is required to use the specific format.

Example manifest.tsv:

FileType fastq Read submission file type sample study instrument_model library_name library_source library_selection library_strategy library_layout forward_file_name forward_file_md5 reverse_file_name reverse_file_md5

The Metadata File

The second component of a successful submission is the Metadata file. This tab delimited file contains all the information about the submitted samples. It is submitted via the “Register Samples” option. Create a file named metadata.tsv or download a spreadsheet template from Webin Submission Portal alike Manifest. Note that the template varies depending on the specific checklist (e.g., GSC MIxS soil, Virus pathogen reporting standard) that matches your sample type. For submitting SARS-CoV-2, the respective checklist is ERC000033 (ENA virus pathogen reporting standard checklist)

Example metadata.tsv:

Checklist ERC000033 ENA virus pathogen reporting standard checklist tax_id scientific_name sample_alias sample_title sample_description collection date geographic location (country and/or sea) host common name host subject id host health state host sex host scientific name collector name collecting institution isolate common name

Summarized Steps for Success

  • Establish FTP connection with ENA.
  • Upload the fastq files (Drag’n’Drop)
  • Login to Webin Submission Portal
  • Upload manifest.tsv through “Submit Reads”
  • Upload metadata.tsv through “Register Samples”
  • Win