BioConvert: a comprehensive format converter for life sciences

Hugo Caro (1) , Sulyvan Dollin (2) , Anne Biton (2) , Bryan Brancotte (2) , Dimitri Desvillechabrol (1, 2) , Yoann Dufresne (3, 2) , Blaise Li (2) , Etienne Kornobis (1, 2) , Frédéric Lemoine (2, 4) , Nicolas Maillet (2) , Amandine Perrin (2, 5) , Nicolas Traut (6) , Bertrand Néron (2) , Thomas Cokelaer (1, 2)

1 Biomics (plateforme technologique)
2 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
3 Algorithmes pour les séquences biologiques - Sequence Bioinformatics
4 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses
5 Génomique évolutive des Microbes / Microbial Evolutionary Genomics
6 NAAT - Neuroanatomie Appliquée et Théorique / Applied and Theoretical Neuroanatomy

Abstract Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the suitable format, which is often a complex, technical and time consuming task. Moreover, these small yet important tasks are often difficult to make reproducible. To overcome these difficulties, we initiated BioConvert, a collaborative project to facilitate the conversion of life science data from one format to another. BioConvert aggregates existing software within a single framework and complemented them with original code when needed. It provides a common interface to make the user experience more streamlined instead of having to learn tens of them. Currently, BioConvert supports about 50 formats and 100 direct conversions in areas such as alignment, sequencing, phylogeny, and variant calling. In addition to being useful for end-users, BioConvert can also be utilized by developers as a universal benchmarking framework for evaluating and comparing numerous conversion tools. Additionally, we provide a web server implementing an online user-friendly interface to BioConvert, hence allowing direct use for the community.

Domains: Bioinformatics [q-bio.QM]; Data Structures and Algorithms [cs.DS]

Hugo Caro, Sulyvan Dollin, Anne Biton, Bryan Brancotte, Dimitri Desvillechabrol, et al.. BioConvert: a comprehensive format converter for life sciences. NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩. ⟨pasteur-04279554v2⟩