Abstract
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3′-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.
Funder
UK Motor Neurone Disease Association and Masonic Charitable Foundation PhD Studentship
American Cancer Society
Blavatnik Family Fellowship in Biomedical Research and by NHLBI of the National Institutes of Health (NIH) under award number
The Emerging Human Brain Cluster (Clúster Emergent del Cervell Humà – CECH) project
European Regional Development Fund of the European Union
Catalan Government
Singapore International Graduate Award. OpenEBench is partly funded by the Horizon 2020 ELIXIR-CONVERGE programme
Swiss National Science Foundation
Publisher
Cold Spring Harbor Laboratory
Cited by
4 articles.
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