SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines

Abstract

Abstract Background The initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initial version of SEDA lacks a command-line interface for more advanced users and does not allow the creation of automated analysis pipelines. Results The present paper discusses the updates of the new SEDA release, including the addition of a complete command-line interface, new functionalities like gene annotation, a framework for automated pipelines, and improved integration in Linux environments. Conclusion SEDA is an open-source Java application and can be installed using the different distributions available ( https://www.sing-group.org/seda/download.html ) as well as through a Docker image ( https://hub.docker.com/r/pegi3s/seda ). It is released under a GPL-3.0 license, and its source code is publicly accessible on GitHub ( https://github.com/sing-group/seda ). The software version at the time of submission is archived at Zenodo (version v1.6.0, http://doi.org/10.5281/zenodo.10201605 ).

Keywords

• FASTA
• Reproducibility
• Pipelines
• Workflows
• Docker