View the Project on GitHub COG-UK/docs

Updated 2021-05-17 by @samstudio8

Consensus sequence uploads to ENA

Following a huge effort from CLIMB-COVID, ENA and WSI; CLIMB-COVID can now automatically submit consensus sequences to ENA and the INSDC on your behalf.

What do I need to do?

Opt in

Previously users were required to opt-in to ENA assembly uploads, however as of 2023-04-27 this process is now automatic and users are automatically opted-in.

Provide basic bioinformatics information

The metadata uploader and Ocarina now have optional fields for describing the bioinformatics pipeline used to process the sequence:

These fields do not (currently) use a controlled vocabulary – please send your comments and concerns about this to #metadata and not DIPI or the Data Working Group. We do however recommend using the following entries for commonly used pipelines:

Pipeline bioinfo_pipe_name bioinfo_pipe_version
ARTIC pipeline tools (ONT) ARTIC fieldbioinformatics (minimap2/nanopolish) X.Y.Z (nanopolish X.Y.Z)
ARTIC Connor Lab Nextflow (Illumina) ncov2019-artic-nf (BWA/ivar) X.Y.Z (ivar X.Y.Z)
ARTIC Connor Lab Nextflow (ONT) ncov2019-artic-nf (fieldbioinformatics/minimap2/nanopolish) X.Y.Z (nanopolish X.Y.Z)

This list will be updated for additional pipelines as needed.

For further information see the CGPS uploader documentation, or the Majora/Ocarina documentation.

What will be uploaded?

Unlike GISAID which only receives High QC PASS seqeunces, ENA/INSDC will receive all Basic QC PASS sequences for deposition.

What if I have bad data?

You should use Ocarina to suppress any bad sequences before they are uploaded into public databases.

When will this happen?

ENA consensus depositions occur daily in the working week (Monday - Friday) but sequences are not uploaded immediately to allow some time for errors to be corrected prior to upload to external databases where corrections are much harder. Samples are uploaded 3 days after they are ingested into the CLIMB-COVID dataset.


Published 2021-05-17. Updated 2021-05-17. Page maintainer @samstudio8.