{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:07Z","timestamp":1772165467024,"version":"3.50.1"},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,3,28]],"date-time":"2023-03-28T00:00:00Z","timestamp":1679961600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,3,28]],"date-time":"2023-03-28T00:00:00Z","timestamp":1679961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004115","name":"Gottfried Wilhelm Leibniz Universit\u00e4t Hannover","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004115","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004115","name":"Gottfried Wilhelm Leibniz Universit\u00e4t Hannover","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004115","id-type":"DOI","asserted-by":"publisher"}]},{"name":"L3S Research Center"},{"name":"L3S Research Center"},{"name":"L3S Research Center"},{"DOI":"10.13039\/501100007210","name":"RWTH Aachen University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007210","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007210","name":"RWTH Aachen University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007210","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007210","name":"RWTH Aachen University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007210","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004115","name":"Gottfried Wilhelm Leibniz Universit\u00e4t Hannover","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004115","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Our results show that GVC provides the best trade-off between compression and random access compared to the state of the art:\u00a0it reduces the genotype information size from 758\u00a0GiB down to 890\u00a0MiB on the publicly available 1000\u00a0Genomes Project (phase\u00a03) data, which is 21% less than the state of the art in random-access capable methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/sXperfect\/gvc\/\">https:\/\/github.com\/sXperfect\/gvc\/<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-023-05240-0","type":"journal-article","created":{"date-parts":[[2023,3,28]],"date-time":"2023-03-28T06:03:21Z","timestamp":1679983401000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["GVC: efficient random access compression for gene sequence variations"],"prefix":"10.1186","volume":"24","author":[{"given":"Yeremia Gunawan","family":"Adhisantoso","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Voges","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Rohlfing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viktor","family":"Tunev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens-Rainer","family":"Ohm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rn","family":"Ostermann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,3,28]]},"reference":[{"issue":"7","key":"5240_CR1","doi-asserted-by":"publisher","first-page":"1002195","DOI":"10.1371\/journal.pbio.1002195","volume":"13","author":"ZD Stephens","year":"2015","unstructured":"Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. 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