MUSTA | MUtation and Somatic Tumor Analysis

Introduction

Provides an overview of Musta and introduces the purpose of the user guide.

Overview

Accurate detection and comprehensive analysis of somatic variants are a major task in cancer sample data analysis, which is routinely carried out combining different software packages with specific software dependencies and with the need of laborious and time-consuming data format conversions.

To overcome these limitations, we developed Musta, an end-to-end pipeline to detect, classify and interpret mutations in cancer.

Musta is a Python command-line tool that easily handles matched tumor-normal samples, from variant calling to the deconvolution of mutational signatures, through variant annotation, driver genes detection, pathway analysis, tumor heterogeneity.

Musta’s core is Snakemake-based and was conceived for an easy installation through the Docker platform. A simple Makefile bootstraps Musta, taking care of the installation, configuration and running steps and allowing the execution of the entire pipeline or any individual step depending on the starting data.

Musta is currently used for cancer sample data analysis at the CRS4-NGS Core

Purpose of the User Guide

The purpose of this user guide for Musta is to provide comprehensive and user-friendly documentation that assists users in effectively utilizing Musta.

This user guide serves several essential purposes:

  • Onboarding Users: It serves as a starting point for users who are new to Musta, helping them become familiar with the tool’s features and capabilities.
  • Guidance: The guide offers step-by-step instructions and explanations to guide users through the process of installing, configuring, and using Musta for somatic mutation analysis.
  • Reference: Users can refer to the guide as a reference whenever they have questions about specific commands, options, or how to perform various tasks within Musta.
  • Troubleshooting: The guide includes information on how to troubleshoot common issues and errors that users may encounter during the analysis.
  • Best Practices: It provides best practices and tips for optimizing workflow efficiency, data management, and overall performance when using Musta.
  • Examples and Use Cases: The guide offers practical examples and real-world use cases, enabling users to understand how to apply Musta to their specific research scenarios.
  • FAQs: Frequently Asked Questions are addressed, providing quick solutions to common queries and problems.
  • Accessibility: The user guide enhances the accessibility of Musta, ensuring that users, regardless of their level of expertise, can effectively use the tool.
  • Confidence Building: By providing detailed information and clear instructions, the guide aims to build user confidence in working with Musta and conducting somatic mutation analysis for cancer research.

In summary, the purpose of the user guide is to empower users with the knowledge and resources they need to harness the full potential of Musta for their somatic mutation analysis needs, making the process smoother and more effective.

Authors and Contacts

Musta is developed by Rossano Atzeni and Matteo Massidda

For bug reports or feature request:

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