Sequencing data resources have increased exponentially in recent years, as has interest in large-scale meta-analyses of integrated next-generation sequencing datasets. However, curation of integrated datasets that match a users particular research priorities is currently a time-intensive and imprecise task. MetaSeek is a sequencing data discovery tool that enables users to flexibly search and filter on any metadata field to quickly find the sequencing datasets that meet their needs. MetaSeek automatically scrapes metadata from all publicly available datasets in the Sequence Read Archive, cleans and parses messy, user-provided metadata into a structured, standard-compliant database, and predicts missing fields where possible. MetaSeek provides a web-based graphical user interface and interactive visualization dashboard, as well as a programmatic API to rapidly search, filter, visualize, save, share, and download matching sequencing metadata.