Whole genome shotgun based next generation transcriptomics and metagenomics studies often generate 100 to 1000 gigabytes (GB) sequence data derived from tens of thousands of different genes or microbial species. De novo assembling these data requires an ideal solution that both scales with data size and optimizes for individual gene or genomes. Here we developed an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions the reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomics and metagenomics test datasets from both short read and long read sequencing technologies. It achieved a near linear scalability with respect to input data size and number of compute nodes. SpaRC can run on different cloud computing environments without modifications while delivering similar performance. In summary, our results suggest SpaRC provides a scalable solution for clustering billions of reads from the next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar big data genomics problems.