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

PLoS Comput Biol. 2016 Jun 16;12(6):e1004937. doi: 10.1371/journal.pcbi.1004937. eCollection 2016 Jun.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / education*
  • Data Interpretation, Statistical
  • Education
  • High-Throughput Nucleotide Sequencing / statistics & numerical data*
  • Humans
  • Teaching

Grants and funding

Funding for this event was provided by the COST action SeqAhead (BM1006) and ELIXIR-UK, which is supported by BBSRC, MRC, and NERC. Bastian Schiffthaler and Nicolas Delhomme are supported by the Wallenberg foundation. Gabriella Rustici and the Bioinformatics Training Facility of the University of Cambridge are supported by the BBSRC and the MRC Doctoral Training Programs. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.