Open AccessSoftware testing in microbial bioinformatics: a call to action
Author(s) -
Boas C.L. van der Putten,
CI Mendes,
Brooke M Talbot,
Jolinda de Korne-Elenbaas,
Rafael Mamede,
Pedro Vila-Cerqueira,
Luís Pedro Coelho,
Christopher A. Gulvik,
Lee S. Katz,
The Asm Ngs Hackathon Participants
Publication year - 2022
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000790
Subject(s) - software engineering , computer science , software , data science , programming language
Computational algorithms have become an essential component of research, with great efforts by the scientific community to raise standards on development and distribution of code. Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics. We have developed these recommendations based on our experience from a collaborative hackathon organised prior to the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference. We also present a repository hosting examples and guidelines for testing, available from https://github.com/microbinfie-hackathon2020/CSIS.