Submitting data to the European Nucleotide Archive (ENA)

There are clear instructions for how to upload data to ENA here.

For environmental/metagenomic data you can find the appropriate taxid you can use here (e.g. the "human gut metagenome" is 408170 or "human saliva metagenome" is 1679718) by exploring the "Tax tree". (There are guidelines on the "Environmental" taxonomy here.

Aspera is a fast way to upload data to ENA (see description here). Note that you will need to install this program for your local user by downloading it from here (change the version to linux if you want to upload from Kronos or Vulcan).

You must do things in a particular order for ENA:

• First, you will need to create an account and then register a study.
• Next, you need to register your samples. It can be very picky about the fields, so I recommend using the "Download spreadsheet to register samples" option. For human-associated studies, you will want to pick "Environmental checklists" > "GSC MIxS human associated"/e.g. "GSC MIxS human oral". You should copy all of your sample names into this sheet, and fill out the other data columns. For some of these, what you fill in will need to be in a specific format (you can see this in the fields that you can check/uncheck when downloading the spreadsheet). If you are giving a date range that "/" between the dates seems to work (e.g. "2009/2015"), but not a colon. You can also add additional metadata fields to this sheet. Save this and then click "Upload filled spreadsheet to register samples".
• After this, you'll want to upload the files. You can see more information on this here. But basically, you can install the Aspera CLI with conda: conda install hcc::aspera-cli. And then you just need to upload your sequencing files, e.g.: ascp -QT -L- sequences_for_upload_Jan2024/* [email protected]:. (it will prompt you to enter your password). These will take a while to be fully visible, but you can check the "Run Files Report" page and filter to Active/Completed to see as files are added to the permanent archive.