FlowOMICC

Purpose

This repository provides a set of Nextflow pipelines that can be used to analyse data generated by the GenOMICC project.

Even though our main dataset consists of GenoMICC data, for historical reasons (COVID-19 pandemic), we have a total of 4 different cohorts: GenOMICC, MILD, REACT and ISARIC. MILD, REACT and ISARIC were integrated in order to provide non severe "controls" for various COVID-19 susceptibility studies.

GenOMICC (Genetics Of Mortality In Critical Care)

Link to the study webpage: https://genomicc.org/.

GenOMICC UK

Inclusion criteria:

Intensive Care Unit patients
UK (mostly England and some specific recruitment centers if I understand correctly)

Additional Information:

The study also seems to be recruiting controls by matching in some way according to this page.
Nurses select who they think might be eligible which could produce cryptic bias as well.

GenOMICC International

This is still being deployed and is not part of our current data.

ISARIC

Link to the study webpage: https://isaric.org/.

Inclusion criteria:

Our subset of individuals all had Covid-19

Additional Information:

The severity varies and a severity score is provided
Many biological and contextual covariates exist but are sparse

MILD

Link to the study webpage: ?

Inclusion criteria:

Covid-19
Volunteers (It is not clear in what way?)
Not hospitalised

REACT (Real-time Assessment of Community Transmission)

Link to the study webpage https://www.imperial.ac.uk/medicine/research-and-impact/groups/react-study/.

Inclusion criteria:

Covid-19
It is unclear if they were hospitalised
It is unclear what the selection process is

Available Workflows

These workflows will typically be run sequentially.