Background. Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing processing tools in bioinformatics pipelines. Further, these frameworks do not have native support for application containers, which are becoming popular in scientific data processing. Results. Here we present MaRe, a programming model with an associated open-source implementation, which introduces support for application containers in MapReduce. MaRe is based on Apache Spark and Docker, the MapReduce framework and container engine that have collected the largest open source community, thus providing interoperability with the cutting-edge software ecosystem. We demonstrate MaRe on two data-intensive applications in life science, showing ease of use and scalability. Conclusions. MaRe enables scalable data-intensive processing in life science with MapReduce and application containers. When compared with current best practices, that involve the use of workflow systems, MaRe has the advantage of providing data locality, ingestion from heterogeneous storage systems and interactive processing. MaRe is generally-applicable and available as open source software.