The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer specific research questions.