COG-UK Docs

View the Project on GitHub COG-UK/docs

Updated 2021-01-11 by @samstudio8

Suppressing sequences inside COG

When to suppress sequences through the API

You should use the Ocarina client to suppress sequences from the COG data set if:

What happens when sequences are suppressed through the API

Sequences marked as suppressed will effectively disappear from the downstream data set. The sequence on Majora will be marked as suppressed. Currently, suppressing a sequence with the API will not remove it from either GISAID nor ENA. You must arrange for sequences to be removed from GISAID by contacting them directly. This will forever mark a (central_sample_id, run_name) pair as suppressed. If you want to replace a sequence without re-sequencing, you will need to upload a new run, and alter the run_name slightly.

How to suppress a sequence

0. Install Ocarina

Run the following command in your shell. You should be running python 3.7 and have pip installed. Feel free to do this from a virtualenv or conda environment.

pip install git+https://github.com/samstudio8/ocarina.git

This will install the latest version of Ocarina, which almost always works.

1. Configure Ocarina

See the Ocarina README for configuration instructions. You will need your API key from your Majora profile. The suppression API does not use OAuth yet.

2. Work out which Published Artifact Groups to suppress

When a sequence and biosample are united by Elan, the result is pushed to Majora and called a “Published Artifact Group” (PAG, for short). PAGs are used to help distinguish sequences generated from the same sample, whether by multiple sequencing centres, multiple runs, or both. PAGs are named in a predictable format, and you’ll need to specify the exact PAG name to suppress your sequence. The format is as follows:

COG-UK/<SAMPLE_NAME>/<SEQUENCING_CENTRE>:<RUN_NAME>

For example: COG-UK/BIRM-655FB/BIRM:20201012_1249_X1_FAO87316_8ae32d4f.

You can use the Groups tab on your Majora profile to help locate the PAG name (or names). Once identified, you can suppress the PAGs using the Ocarina client.

3. Suppress

Using the ocarina pag suppress command, pass your list of PAGs to suppress:

ocarina pag suppress --reason XXXX --publish-group 'COGUK\SAMPLE1\SITE:MY_FIRST_RUN' 'COGUK/SAMPLE2/SITE:MY_FIRST_RUN'

You must choose a reason to suppress with --reason, which can be one of the following: WRONG_BARCODE, WRONG_METADATA, WRONG_SEQUENCE, CONTROL_FAIL.

The API will respond with any problems inside the messages list. If you’re using Ocarina, this will automatically be printed to your terminal. You can verify the PAG has been suppressed via the Majora web interface.


Published 2020-12-09. Updated 2021-01-11. Page maintainer @samstudio8.