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BACKGROUND: In recent years, advances in high-throughput sequencing technologies have enabled the use of genomic information in many fields, such as precision medicine, oncology, and food quality control. The amount of genomic data being generated is growing rapidly and is expected to soon surpass the amount of video data. The majority of sequencing experiments, such as genome-wide association studies, have the goal of identifying variations in the gene sequence to better understand phenotypic variations. We present a novel approach for compressing gene sequence variations with random access capability: the Genomic Variant Codec (GVC). We use techniques such as binarization, joint row- and column-wise sorting of blocks of variations, as well as the image compression standard JBIG for efficient entropy coding. RESULTS: Our results show that GVC provides the best trade-off between compression and random access compared to the state of the art: it reduces the genotype information size from 758 GiB down to 890 MiB on the publicly available 1000 Genomes Project (phase 3) data, which is 21% less than the state of the art in random-access capable methods. CONCLUSIONS: By providing the best results in terms of combined random access and compression, GVC facilitates the efficient storage of large collections of gene sequence variations. In particular, the random access capability of GVC enables seamless remote data access and application integration. The software is open source and available at https://github.com/sXperfect/gvc/ .

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A new set of three-dimensional (3D) data formats and associated compression technologies are emerging with the aim to achieve more flexible representation and higher compression of 3D and multiview video content. These new tools will facilitate the generation of multiview output (e.g., as needed for multiview auto-stereoscopic displays), provide richer immersive multimedia experiences, and allow new interactive applications. This special section includes a timely set of papers covering the most recent technical developments in this area with papers covering topics in the different aspects of 3D systems, from representation and compression algorithms to rendering techniques and quality assessment. This special section includes a good balance on topics that are of interest to academic, industrial, and standardization communities. We believe that this collection of papers represent the most recent advances in representation, compression, rendering, and quality assessment of 3D scenes.

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Three-dimensional (3-D) subband/wavelet coding with motion compensation has been demonstrated to be an efficient technique for video coding applications in some recent research works. When motion compensation is performed with half-pixel accuracy, images need to be interpolated in both temporal subband analysis and synthesis stages. The resulting subband filter banks developed in these former algorithms were not invertible due to image interpolation. In this paper, an invertible temporal analysis/synthesis system with half-pixel-accurate motion compensation is presented. We look at temporal decomposition of image sequences as a kind of down-conversion of the sampling lattices. The earlier motion-compensated (MC) interlaced/progressive scan conversion scheme is extended for temporal subband analysis/synthesis. The proposed subband/wavelet filter banks allow perfect reconstruction of the decomposed video signal while retaining high energy compaction of subband transforms. The invertible filter banks are then utilized in our 3-D subband video coder. This video coding system does not contain the temporal DPCM loop employed in the conventional hybrid coder and the earlier MC 3-D subband coders. The experimental results show a significant PSNR improvement by the proposed method. The generalization of our algorithm for MC temporal filtering at arbitrary subpixel accuracy is also discussed.

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