EBI submission via Qiita

Qiita allows users to deposit their study, sample, experiment and sequence data to the European Nucleotide Archive (ENA), which is the permanent data repository of the European Bioinformatics Institute (EBI). Submitting to this repository will provide you with a unique identifier for your study, which is generally a requirement for publication. Your study will be housed with all other Qiita submissions and so we require adherence to the MiXs standard.

EBI/ENA requires a given set of column fields to describe your samples and experiments, for more information visit Prepare information files and pay most attention to EBI required fields, without these Qiita Admins will not be able to submit. If you want to submit your data or need help send an email to qiita.help@gmail.com. Help will include advice on additional fields to add to ensure MiXs compliance.

Note that submissions are time consuming and need full collaboration from the user. Do not wait until the last minute to request help. In general, the best time to request a submission is when you are writing your paper. Remember that the data can be submitted to EBI and can be kept private and simply make public when the paper is accepted. Note that EBI/ENA takes up to 15 days to change the status from private to public, so consider this when submitting data and your manuscript.


For convenience Qiita allows you to upload a QIIME mapping file to process your data. However, the QIIME mapping file, in general, doesn’t have all the EBI/ENA fields. Thus, you will need to update your information files (sample or preparation) via the update option. To simplify this process, you can download the system generated files and add/modify these fields for each file.