In this paper, we present HPMA, a graphics processing unit (GPU) accelerated meta-genome sequence alignment algorithm for a collection of DNA sequences. This algorithm supports all-to-all pairwise local alignment on NVIDIA GPUs. HPMA builds on an GPU alignment algorithm that we developed earlier with the addition of a filter module. We designed and developed this new kernel function based on the suffix array data structure. The filter module improves performance by identifying a subset of sequences which meet a user-defined similarity threshold and should be considered for alignment. HPMA has the ability to balance the workload between CPU and GPU. HPMA allows us to preprocess massively large metagenomes in a reasonable amount of time in response to increasing speed of NGS sequencers. The performance of HPMA has been evaluated on a cluster of Kepler-based Tesla K20 GPUs using a variety of short DNA sequence datasets.