. . . . . "assembler developer" . "GigaScience journal" . . . "programming" . . "Case Study" . . "reproducibility study" . . "href" . . "Alejandra Gonzalez-Beltran" . . "59628"^^ . "https://api.rohub.org/api/ros/7b766778-d12f-45b3-bb71-ab4e95cbbc2c/crate/download/" . . . "2014-08-01 09:02:25.154000+00:00" . "2025-10-18 11:55:12.696752+00:00" . "2014-08-01 09:02:25.154000+00:00" . "The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing data models and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the SOAPdenovo2 de novo genome assembler. The case study was a joint effort by the GigaScience journal, the Investigation/Study/Assay (ISA), Nanopublication (Nanopub) and Research Object (RO) communities and SOAPdenovo2 de novo genome assembler developers.\r\nSee source: http://isa-tools.github.io/soapdenovo2/" . "application/ld+json" . . . . . . "https://w3id.org/ro-id/7b766778-d12f-45b3-bb71-ab4e95cbbc2c" . . "SOAPdenovo2 Case Study RO" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "Try clicking \"Show all\" to see all the annotations (e.g., creators, contributors) on the RO." . "Raul Palma, Jun Zhao, Marco Roos, Maria Susana Avila-Garcia, Mark Thompson, Peter Li, Philippe Rocca-Serra, et al. \"SOAPdenovo2 Case Study RO.\" ROHub. Aug 01 ,2014. https://w3id.org/ro-id/7b766778-d12f-45b3-bb71-ab4e95cbbc2c." . "isa-owl" . . . "nanopubs" . . . "Outputs" . . . "Workflows" . . . "ro-description" . . . "isa-tab" . . . "NanoStm" . . . . . . "ro" . . . . . . "mathematics" . . "1.3559322033898304" . "1.2" . "information" . . "4.436229205175601" . "9.6" . "title" . . "2.36550934757726" . "6.2" . "software location" . . "1.6577060931899643" . "3.7" . "space sciences (general)" . . "10.050736682322816" . "0.10134920477867126" . "law" . . "2.824858757062147" . "2.5" . "sequence assembly algorithm" . . "1.478494623655914" . "3.3" . "software" . . "4.845478824876001" . "12.7" . "reproducibility study" . . "5.913978494623656" . "13.2" . "http" . . "9.996184662342616" . "26.2" . "source" . . "2.1747424647081264" . "5.7" . "investigation person role" . . "0.8512544802867384" . "1.9" . "SOAPdenovo2" . . "22.96672828096118" . "49.699999999999996" . "biology" . . "3.0508474576271185" . "2.7" . "geosciences" . . "89.94926331767718" . "0.9070266783237457" . "study publication status term accession number" . . "0.9856630824372762" . "2.2" . "The case study was a joint effort by the GigaScience journal, the Investigation/Study/Assay (ISA), Nanopublication (Nanopub) and Research Object (RO) communities and SOAPdenovo2 de novo genome assembler developers." . . "17.517564402810304" . "37.4" . "investigation title investigation" . . "0.8960573476702509" . "2.0" . "href" . . "4.006104540251812" . "10.5" . "genome assembler developer" . . "1.5681003584229392" . "3.5" . "repository" . . "3.696857670979667" . "8.0" . "assembler developer" . . "12.32078853046595" . "27.5" . "publication" . . "2.4029574861367835" . "5.2" . "Investigation Publication Status Term Source REF\t\"\"" . . "2.154566744730679" . "4.6" . "GitHub repository" . . "39.112903225806456" . "87.3" . "data producer" . . "2.0332717190388174" . "4.4" . "assembler" . . "3.3733826247689462" . "7.3" . "software" . . "14.915254237288135" . "13.2" . "Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy." . . "2.34192037470726" . "5.0" . "investigation publication status term source ref" . . "1.8369175627240142" . "4.1" . "software" . . "3.9741219963031424" . "8.6" . "Medicine" . . "Health/Health treatment/Medicine" . "term accession number" . . "1.388888888888889" . "3.1" . "publication" . . "6.409767264402898" . "16.799999999999997" . "Genetics" . . "Science and technology/Natural science/Biology/Genetics" . "investigation" . . "8.470049599389545" . "22.2" . "http" . . "11.367837338262477" . "24.6" . "computer science" . . "12.429378531073446" . "11.0" . "Genetics" . . "Science and technology/Natural science/Biology/Genetics" . "Science and technology" . . "Science and technology" . "Language" . . "Arts, culture and entertainment/Culture/Language" . "Gigascience" . . "2.2181146025878005" . "4.8" . "case study RO." . . "11.021505376344086" . "24.6" . "Internet" . . "4.858757062146893" . "4.3" . "earth resources and remote sensing" . . "89.94926331767718" . "0.9070266783237457" . "Investigation Title\t\"Investigation\"" . . "1.9203747072599529" . "4.1" . "Tak" . . . "Oxford" . . "1.8313620755436855" . "4.8" . "RO." . . "2.9112754158964878" . "6.3" . "Library and museum" . . "Arts, culture and entertainment/Culture/Library and museum" . "anthropology" . . "1.92090395480226" . "1.7" . "For more information, please visit:\n\nhttp://isa-tools.github.io/soapdenovo2/" . . "9.36768149882904" . "20.0" . "People" . . "Human interest/People" . "publishing" . . "3.615819209039548" . "3.2" . "software script" . . "2.060931899641577" . "4.6" . "computer programming" . . "43.84180790960451" . "38.8" . "investigation" . . "4.990757855822551" . "10.8" . "algorithm" . . "2.937809996184662" . "7.7" . "the 2008" . . "Shenzhen" . . . "Oxford" . . . "GitHub repository for the SOAPdenovo2 case study." . . "27.02576112412178" . "57.7" . "workflow enactment engine" . . "7.168458781362007" . "16.0" . "information technology" . . "11.186440677966102" . "9.9" . "Software" . . "Economy, business and finance/Economic sector/Computing and information technology/Software" . "earth sciences" . . "39.34946938216159" . "0.7937774062156677" . "SOAPdenovo2\n===========" . . "10.398126463700235" . "22.2" . "environmental sciences" . . "17.79124472514932" . "0.3588939905166626" . "algorithm" . . "2.5415896487985212" . "5.5" . "earth sciences" . . "42.859285892689094" . "0.8645792007446289" . "See source: http://isa-tools.github.io/soapdenovo2/" . . "6.182669789227166" . "13.2" . "SOAPdenovo2 Case Study RO. The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing data models and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the SOAPdenovo2 de novo genome assembler." . . "23.091334894613585" . "49.3" . "University of Hong Kong" . . "1.9408502772643252" . "4.2" . "Interior" . . . "investigation identifier" . . "0.8512544802867384" . "1.9" . "oceanography" . . "42.859285892689094" . "0.8645792007446289" . "genome" . . "3.6506469500924212" . "7.9" . "Library and museum" . . "Arts, culture and entertainment/Culture/Library and museum" . "space sciences" . . "10.050736682322816" . "0.10134920477867126" . "case study" . . "11.922365988909426" . "25.8" . "case study" . . "10.873712323540632" . "28.5" . "genome" . . "6.409767264402899" . "16.8" . "GitHub" . . "9.380776340110906" . "20.3" . "geology" . . "39.34946938216159" . "0.7937774062156677" . "programmer" . . "2.1365890881342997" . "5.6" . "Chemistry" . . "Science and technology/Natural science/Chemistry" . "research center" . . "1.9839755818389926" . "5.2" . "information" . . "4.311331552842426" . "11.3" . "ecological applications" . . "17.79124472514932" . "0.3588939905166626" . "Tab" . . "1.907668828691339" . "5.0" . "Wireless technology" . . "Economy, business and finance/Economic sector/Computing and information technology/Wireless technology" . "Genetics" . . "Science and technology/Natural science/Biology/Genetics" . "communication protocol" . . "2.212895841281953" . "5.8" . "assembler" . . "5.227012590614269" . "13.7" . "repository for the SOAPdenovo2 case study" . . "5.645161290322581" . "12.6" . "workflow" . . "1.7932086989698586" . "4.7" . "investigation publication author list" . . "0.8960573476702509" . "2.0" . "Oxford University" . . . "investigation publication DOI" . . "0.8512544802867384" . "1.9" . "href" . . "4.205175600739372" . "9.1" . "status" . . "1.9870609981515712" . "4.3" . "term source ref" . . "1.5681003584229392" . "3.5" . "study" . . "2.098435711560473" . "5.5" . "Anthropology" . . "Science and technology/Social sciences/Anthropology" . "Raul Palma" . . "service-account-enrichment" . . "service-account-generation-service" . . . "2025-11-11T16:45:10.171+01:00"^^ . . . "SOAPdenovo2 Case Study RO" . "RSA" . "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA4pPaESKwmC6l37P86K6TNLq6yeQtc7m9CvcqauLs/1FC0viHvQnFBgxj0a+loPDv/Egwe6OqFpa0iW9Ypnyz9YPoh+pxbRXonbuMOb+8Ry9hXZ+TEKfWjhjVDGEaClwfRwglh2HI/xfV4CD9AgvDOEoZQiyta8a90PYwJ3G6e70oCHTn61+OWTkI9KRYHOYgg3btdy2Z7q/30PTFawb2ZT5aIfIJYobUYv2a7yhtcqWCHZeKv0bxGnRjTFNx1rscBMlLJSzvRtpQc1cCRVEPFZHo1adaXCI9tGvn4cxeNQ96y8dxkN1XhpaJairde+23MDzf42Oe97KG2HYzKiyVnQIDAQAB" . 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