| layout | title | date_published | date_modified | author | maintainer |
|---|---|---|---|---|---|
docpost |
Consensus sequence uploads to ENA |
2021-05-17 10:50:00 +0000 |
2021-05-17 11:30:00 +0000 |
samstudio8 |
samstudio8 |
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.
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.
The metadata uploader and Ocarina now have optional fields for describing the bioinformatics pipeline used to process the sequence:
bioinfo_pipe_namebioinfo_pipe_version
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.
Unlike GISAID which only receives High QC PASS seqeunces, ENA/INSDC will receive all Basic QC PASS sequences for deposition.
You should use Ocarina to suppress any bad sequences before they are uploaded into public databases.
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.
- 2023-09-06: Upload lag changed to 3 days, down from >7 days.
- 2023-12-04: Consensus fasta sequences are now sanitised on upload to ENA to remove illegal characters (characters except: A, C, G, T, a, c, g, t, N)