An Open Framework for Extensible Multi-Stage Bioinformatics Software

TL;DR

This paper introduces Friedrich, an extensible bioinformatics framework built on Scala, enabling flexible, high-performance workflows suitable for both experimentation and batch processing, thus enhancing developer productivity.

Contribution

It presents a novel software framework that balances customisability and performance in bioinformatics workflows, using a multiparadigm language for flexibility.

Findings

Supports both experimentation and batch processing

Demonstrated with a genome assembler case study

Potential to increase bioinformatics software development productivity

Abstract

In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance. Performance-sensitive tools are often highly monolithic, which can make research difficult. We present a novel set of software development principles and a bioinformatics framework, Friedrich, which is currently in early development. Friedrich applications support both early stage experimentation and late stage batch processing, since they simultaneously allow for good performance and a high degree of flexibility and customisability. These benefits are obtained in large part by basing Friedrich on the multiparadigm programming language Scala. We present a case study in the form of a basic genome assembler and its extension with new functionality. Our architecture has the potential to greatly increase the overall productivity of software developers and researchers in bioinformatics.