COV-IRT Pipeline Subgroup
The pipeline subgroup develops consensus pipelines for processing raw data related to the COVID-19 pandemic, which will subsequently be used by other COV-IRT subgroups for downstream analyses. This ensures that all COV-IRT subgroups performing downstream analyses are able to leverage data that has been harmonized using a set of standardized pipelines, thereby eliminating technical biases that may arise as a result of using different tools and algorithms.
This repository contains the processing pipelines that have been standardized to date for the assay types indicated below. Each subdirectory holds the pipeline used to process raw data derived from the respective assay type, including detailed descriptions of each step as well as the exact commands used to generate processed data for different cohorts of samples analyzed by COV-IRT.
Click on an assay type below for data processing information.