{"id":"https://openalex.org/W2956124022","doi":"https://doi.org/10.5220/0004881002150220","title":"De Novo Short Read Assembly Algorithm with Low Memory Usage","display_name":"De Novo Short Read Assembly Algorithm with Low Memory Usage","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2956124022","doi":"https://doi.org/10.5220/0004881002150220","mag":"2956124022"},"language":"en","primary_location":{"id":"doi:10.5220/0004881002150220","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004881002150220","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0004881002150220","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019202076","display_name":"Yuki Endo","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yuki Endo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053688490","display_name":"Fubito Toyama","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fubito Toyama","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021202926","display_name":"Chikafumi Chiba","orcid":"https://orcid.org/0000-0002-7767-2150"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chikafumi Chiba","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087914771","display_name":"Hiroshi Mori","orcid":"https://orcid.org/0000-0003-0806-7704"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hiroshi Mori","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5100854680","display_name":"Kenji Shoji","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kenji Shoji","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5019202076"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26680624,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"215","last_page":"220"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9690999984741211,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9408000111579895,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.738196611404419},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.718126118183136},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5706654787063599},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5586823225021362},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4958213269710541},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.4452270567417145},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3605308532714844},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1790165901184082},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17134007811546326},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12722483277320862},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08556851744651794}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.738196611404419},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.718126118183136},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5706654787063599},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5586823225021362},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4958213269710541},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.4452270567417145},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3605308532714844},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1790165901184082},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17134007811546326},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12722483277320862},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08556851744651794},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5220/0004881002150220","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004881002150220","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.5220/0004881002150220","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004881002150220","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","score":0.6700000166893005,"display_name":"Zero hunger"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2484133401","https://openalex.org/W2115501618","https://openalex.org/W2127768708","https://openalex.org/W3215016332","https://openalex.org/W2013652688","https://openalex.org/W2163830511","https://openalex.org/W2061214760","https://openalex.org/W2159998739","https://openalex.org/W2268029186","https://openalex.org/W2165847428"],"abstract_inverted_index":{"Determining":[0],"whole":[1,38],"genome":[2,39],"sequences":[3],"of":[4,26,58,93,104,116,155,161],"various":[5],"species":[6],"has":[7,31,100],"many":[8],"applications":[9],"not":[10],"only":[11],"in":[12,16,88,102],"biological":[13],"system,\r\n\r\nbut":[14],"also":[15],"medicine,":[17],"pharmacy":[18],"and":[19,35,106],"agriculture.":[20],"In":[21,131,145],"recent":[22,89],"years,":[23],"the":[24,52,94,114,156],"emergence":[25],"high-throughput":[27],"next":[28],"generation\r\n\r\nsequencing":[29],"technologies":[30,42],"dramatically":[32],"reduced":[33],"time":[34,107],"costs":[36],"for":[37,63,82,138],"sequencing.\r\n\r\nThese":[40],"new":[41],"provide":[43],"ultrahigh":[44],"throughput":[45],"with":[46,128,142],"lower":[47,143],"unit":[48],"data":[49,53,74],"cost.":[50],"However,":[51],"are":[54],"very\r\n\r\nshort":[55],"length":[56],"fragments":[57,66,71,118],"DNA.":[59],"Thus,":[60],"developing":[61],"algorithms":[62,81],"merging":[64],"these":[65,70],"is":[67,75,96,119,123],"very":[68],"important.\r\n\r\nMerging":[69],"without":[72],"reference":[73],"called":[76],"de":[77,83,139],"novo":[78,140],"assembly.":[79],"Many":[80],"novo\r\n\r\nassembly":[84],"have":[85],"been":[86],"proposed":[87,157],"years.":[90],"Velvet,":[91],"one":[92],"algorithms,":[95],"famous":[97],"because":[98],"it":[99,122],"good\r\n\r\nperformance":[101],"terms":[103],"memory":[105,110,153],"consumption.":[108],"But":[109],"consumption":[111,154],"increases":[112],"dramatically\r\n\r\nwhen":[113],"size":[115],"input":[117],"huge.":[120],"Therefore,":[121],"necessary":[124],"to":[125],"develop":[126],"algorithm":[127,137,158],"low":[129],"memory\r\n\r\nusage.":[130],"this":[132],"paper,":[133],"we":[134],"propose":[135],"an":[136],"assembly":[141],"memory.":[144],"our":[146],"experiments\r\n\r\nusing":[147],"E.coli":[148],"K-12":[149],"strain":[150],"MG":[151],"1655,":[152],"was":[159],"one-third":[160],"that":[162],"of\r\n\r\nVelvet.":[163]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2019-07-12T00:00:00"}
