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.
As with GISAID uploads you must opt-in from your Institute profile. You must fill in the lab name, lab address and lab authors (under the “GISAID and ENA” headers).
The metadata uploader and Ocarina now have optional fields for describing the bioinformatics pipeline used to process the sequence:
bioinfo_pipe_namebioinfo_pipe_versionThese 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.
Unlike GISAID which only receives High QC PASS seqeunces, ENA/INSDC will receive all Basic QC PASS sequences for deposition. Sequences will only be uploaded if:
bioinfo_pipe_name and bioinfo_pipe_versionAs of May 2021, we are currently uploading prospective data. Existing sequences will need the bioinformatics fields backfilled to be eligible for upload and we will work on a solution for this.
You should use Ocarina to suppress any bad sequences before they are uploaded into public databases.
ENA consensus depositions will happen weekly after the ENA raw data has been accessioned to allow for linking.