New genomic technologies, such as exome, whole-genome and transcriptome sequencing, are transforming the genetic diagnosis of neuromuscular diseases and dramatically accelerating the discovery of new disease-associated genes. The increasingly widespread availability of these technologies creates both opportunities and challenges for neuromuscular disease researchers. Here we survey the current literature on the application of new genomic technologies to the diagnosis of severe muscle diseases, with a focus on assessment of the approaches used for data processing, analysis and interpretation. We also highlight several key areas requiring improvement.