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PughLab pipeline suite: MismatchResolveDX

Welcome to the MismatchResolveDX wiki!

This is a collection of pipelines to be used for the MismatchResolveDX targeted-sequencing panel. This panel includes i) conventional DNA-Seq of hereditary cancer genes, ii) EM-Seq for methylation analysis of MMR-related genes and iii) shallow WGS for tumour-fraction estimation.

Installation and Dependencies

Start by creating a clone of the repository:

cd /path/to/some/directory
git clone git@github.com:pughlab/MismatchResolveDX.git

Overview

Table of contents

1. Input file format
2. Workflow (How to start a project)
3. DNA Pipeline
4. Methylation Pipeline
5. sWGS Pipeline
6. Pipeline Summarization
7. MSI Classifier