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Introduciton

A comprehensive bioinformatics pipeline for the large-scale collaborative analysis of Multiple Myeloma genomes in an effort to delineate the broad spectrum of somatic events

The inspiration behind development of the pipeline was 3 major points:

• Generation of consensus variant calls across multiple large WGS datasets
• A singular, consistent, automated workflow that is portable and reproducible across different data centers
• Circumvent need for all data to be centrally located

As a result, this pipeline was written entirely in Nextflow and utilizes Singularity containers to house all processes. This removes all issues stemming from environment incompatibilities, version inconsistencies, missing dependencies, or a need to setup the necessary tools on a user's HPC infrastructure.

The pipeline is divided into 3 modules: Preprocessing, Germline, and Somatic The core instructions for deployment, usage, and expected output of all steps are well laid out on the main page of the repository. This Wiki will provide in-depth provenance and explanation of methods in an effort to give full transparency to the pipeline, its processes, and reference material.

Table of Contents

• Usage
• Reference Genome
• Preprocessing
• Germline
• Somatic