Mars: simplifying bioinformatics workflows through a containerized approach to tool integration and management.

Abstract

Summary: Bioinformatics is a rapidly evolving field with numerous specialized tools developed for essential genomic analysis tasks, such as read simulation, mapping, and variant calling. However, managing these tools presents significant challenges due to varied dependencies, execution steps, and output formats, complicating the installation and configuration processes. To address these issues, we introduce "Mars" a bioinformatics solution encapsulated within a singularity container that preloads a comprehensive suite of widely used genomic tools. Mars not only simplifies the installation of these tools but also automates critical workflow functions, including sequence sample preparation, read simulation, read mapping, variant calling, and result comparison. By streamlining the execution of these workflows, Mars enables users to easily manage input-output formats and compare results across different tools, thereby enhancing reproducibility and efficiency. Furthermore, by providing a cohesive environment that integrates tool management with a flexible workflow interface, Mars empowers researchers to focus on their analyses rather than the complexities of tool configuration. This integrated solution facilitates the testing of various combinations of tools and algorithms, enabling users to evaluate performance based on different metrics and identify the optimal tools for their specific genomic analysis needs. Through Mars, we aim to enhance the accessibility and usability of bioinformatics tools, ultimately advancing research in genomic analysis.

Availability and implementation: Mars is freely available at https://github.com/GenomicAI/mars. It is implemented within a Singularity container environment and supports modular extension for additional genomic tools and custom workflows.