{"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00113050","sets":["934:1151:7875"]},"path":["7875"],"owner":"11","recid":"113050","title":["A Memory Efficient Short Read De Novo Assembly Algorithm"],"pubdate":{"attribute_name":"公開日","attribute_value":"2015-01-27"},"_buckets":{"deposit":"e492dc78-234f-4676-8262-710b598165c1"},"_deposit":{"id":"113050","pid":{"type":"depid","value":"113050","revision_id":0},"owners":[11],"status":"published","created_by":11},"item_title":"A Memory Efficient Short Read De Novo Assembly Algorithm","author_link":["36442","36440","36438","36435","36436","36437","36439","36444","36441","36443"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"A Memory Efficient Short Read De Novo Assembly Algorithm"},{"subitem_title":"A Memory Efficient Short Read De Novo Assembly Algorithm","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"[Original Paper] bioinformatics, next generation sequencing, de novo assembly, de Bruijn graph","subitem_subject_scheme":"Other"}]},"item_type_id":"3","publish_date":"2015-01-27","item_3_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University"},{"subitem_text_value":"Faculty of Life and Environmental Sciences, University of Tsukuba"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University"}]},"item_3_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University","subitem_text_language":"en"},{"subitem_text_value":"Faculty of Life and Environmental Sciences, University of Tsukuba","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Engineering, Utsunomiya University","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/113050/files/IPSJ-TBIO0800002.pdf"},"date":[{"dateType":"Available","dateValue":"2015-01-27"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-TBIO0800002.pdf","filesize":[{"value":"1.5 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Shoji"}],"nameIdentifiers":[{}]}]},"item_3_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Yuki, Endo","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Fubito, Toyama","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Chikafumi, Chiba","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Hiroshi, Mori","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Kenji, Shoji","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_3_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA12177013","subitem_source_identifier_type":"NCID"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_6501","resourcetype":"journal article"}]},"item_3_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1882-6679","subitem_source_identifier_type":"ISSN"}]},"item_3_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"Sequencing the whole genome of various species has many applications, not only in understanding biological systems, but also in medicine, pharmacy, and agriculture. In recent years, the emergence of high-throughput next generation sequencing technologies has dramatically reduced the time and costs for whole genome sequencing. These new technologies provide ultrahigh throughput with a lower per-unit data cost. However, the data are generated from very short fragments of DNA. Thus, it is very important to develop algorithms for merging these fragments. One method of merging these fragments without using a reference dataset is called de novo assembly. Many algorithms for de novo assembly have been proposed in recent years. Velvet and SOAPdenovo2 are well-known assembly algorithms, which have good performance in terms of memory and time consumption. However, memory consumption increases dramatically when the size of input fragments is larger. Therefore, it is necessary to develop an alternative algorithm with low memory usage. In this paper, we propose an algorithm for de novo assembly with lower memory. In our experiments using E.coli K-12 strain MG 1655 and human chromosome 14, the memory consumption of our proposed algorithm was less than that of other popular assemblers.","subitem_description_type":"Other"}]},"item_3_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"Sequencing the whole genome of various species has many applications, not only in understanding biological systems, but also in medicine, pharmacy, and agriculture. In recent years, the emergence of high-throughput next generation sequencing technologies has dramatically reduced the time and costs for whole genome sequencing. These new technologies provide ultrahigh throughput with a lower per-unit data cost. However, the data are generated from very short fragments of DNA. Thus, it is very important to develop algorithms for merging these fragments. One method of merging these fragments without using a reference dataset is called de novo assembly. Many algorithms for de novo assembly have been proposed in recent years. Velvet and SOAPdenovo2 are well-known assembly algorithms, which have good performance in terms of memory and time consumption. However, memory consumption increases dramatically when the size of input fragments is larger. Therefore, it is necessary to develop an alternative algorithm with low memory usage. In this paper, we propose an algorithm for de novo assembly with lower memory. In our experiments using E.coli K-12 strain MG 1655 and human chromosome 14, the memory consumption of our proposed algorithm was less than that of other popular assemblers.","subitem_description_type":"Other"}]},"item_3_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"8","bibliographic_titles":[{"bibliographic_title":"IPSJ Transactions on Bioinformatics （TBIO）"}],"bibliographicPageStart":"2","bibliographicIssueDates":{"bibliographicIssueDate":"2015-01-27","bibliographicIssueDateType":"Issued"},"bibliographicVolumeNumber":"8"}]},"relation_version_is_last":true,"weko_creator_id":"11"},"updated":"2025-01-20T19:48:53.649352+00:00","created":"2025-01-18T23:54:42.222266+00:00","links":{},"id":113050}