Caro Hugo, Dollin Sulyvan, Biton Anne, Brancotte Bryan, Desvillechabrol Dimitri, Dufresne Yoann, Li Blaise, Kornobis Etienne, Lemoine Frédéric, Maillet Nicolas, Perrin Amandine, Traut Nicolas, Néron Bertrand, Cokelaer Thomas
Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France.
Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France.
NAR Genom Bioinform. 2023 Aug 21;5(3):lqad074. doi: 10.1093/nargab/lqad074. eCollection 2023 Sep.
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 , a collaborative project to facilitate the conversion of life science data from one format to another. 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, 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, 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 , hence allowing direct use for the community.
生物信息学是一个因多年来开发的众多标准和格式而闻名的领域。这种过多的格式，有时相互补充，且常常冗余，给生物信息学数据分析人员带来了许多挑战。他们不断需要找到最佳工具将数据转换为合适的格式，这往往是一项复杂、技术含量高且耗时的任务。此外，这些小而重要的任务往往难以实现可重复性。为了克服这些困难，我们启动了一个合作项目，以促进生命科学数据从一种格式转换为另一种格式。该项目在单个框架内整合了现有软件，并在需要时用原创代码对其进行补充。它提供了一个通用接口，以使用户体验更加简化，而不必学习数十种接口。目前，该项目在比对、测序、系统发育和变异检测等领域支持约50种格式和100种直接转换。除了对终端用户有用外，该项目还可被开发人员用作评估和比较众多转换工具的通用基准框架。此外，我们提供了一个实现该项目在线用户友好界面的网络服务器，从而允许社区直接使用。
