Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability

Abstract

The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials would support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers' community. To achieve this, we have developed a strategy for materials' curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at http://bioinformatics.upsc.se/htmr.

Fig 1. Overview of the repository’s implementation, content, search interface, and flowchart of roles and actions.

Authors add their material to the main repository, where they can be searched and retrieved by trainers. Any trainer can then build on existing materials for their own lectures and practicals and request a merge of the updated materials into the main repository, which upon validation, results in the older version of the material to be archived. Two of the consortium members act as curators for each topic, ensuring the completeness of the descriptors and the adequate use of the controlled vocabularies. The newly added materials are then indexed and made discoverable through the search interface. Both the search interface and repository rely on a GitLab instance hosted by the consortium. The Git logo is licensed under CC BY-SA 4.0 by GitLab (https://about.gitlab.com/press/).