Software Open Access
Marcelino, V. R.; Clausen, P.T.C.L; Buchmann, J.P.; Wille, M.; Iredell, J.R.; Meyer, W.; Lund, O.; Sorrell, T.C.; Holmes, E.C.
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R.</foaf:name> <foaf:givenName>V. R.</foaf:givenName> <foaf:familyName>Marcelino</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Clausen, P.T.C.L</foaf:name> <foaf:givenName>P.T.C.L</foaf:givenName> <foaf:familyName>Clausen</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Technical University of Denmark</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Buchmann, J.P.</foaf:name> <foaf:givenName>J.P.</foaf:givenName> <foaf:familyName>Buchmann</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Wille, M.</foaf:name> <foaf:givenName>M.</foaf:givenName> <foaf:familyName>Wille</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The Peter Doherty Institute for Infection and Immunity</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Iredell, J.R.</foaf:name> <foaf:givenName>J.R.</foaf:givenName> <foaf:familyName>Iredell</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Meyer, W.</foaf:name> <foaf:givenName>W.</foaf:givenName> <foaf:familyName>Meyer</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Lund, O.</foaf:name> <foaf:givenName>O.</foaf:givenName> <foaf:familyName>Lund</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Technical University of Denmark</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Sorrell, T.C.</foaf:name> <foaf:givenName>T.C.</foaf:givenName> <foaf:familyName>Sorrell</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Holmes, E.C.</foaf:name> <foaf:givenName>E.C.</foaf:givenName> <foaf:familyName>Holmes</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>The University of Sydney</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:title>CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data</dct:title> <dct:publisher> <foaf:Agent> <foaf:name>Zenodo</foaf:name> </foaf:Agent> </dct:publisher> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2019</dct:issued> <dcat:keyword>metagenomics</dcat:keyword> <dcat:keyword>microbiome</dcat:keyword> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-05-18</dct:issued> <dct:language rdf:resource="http://publications.europa.eu/resource/authority/language/ENG"/> <owl:sameAs rdf:resource="https://zenodo.org/record/3668497"/> <adms:identifier> <adms:Identifier> <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/3668497</skos:notation> <adms:schemeAgency>url</adms:schemeAgency> </adms:Identifier> </adms:identifier> <foaf:page rdf:resource="https://doi.org/10.1101/641332"/> <dct:isVersionOf rdf:resource="https://doi.org/10.5281/zenodo.3668496"/> <owl:versionInfo>1.0.0</owl:versionInfo> <dct:description><p>CCMetagen is a software to identify taxa from metagenome data. This repository contains CCMetagen version 1.0.0, which was benchmarked with other software in the original CCMetagen publication.</p> <p>High-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align individual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Our pipeline substantially outperforms other commonly used software in identifying bacteria and fungi, and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.</p></dct:description> <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/> <dct:accessRights> <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess"> <rdfs:label>Open Access</rdfs:label> </dct:RightsStatement> </dct:accessRights> <dcat:distribution> <dcat:Distribution> <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/> <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.3668497"/> </dcat:Distribution> </dcat:distribution> <dcat:distribution> <dcat:Distribution> <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.3668497"/> <dcat:byteSize>645439</dcat:byteSize> <dcat:downloadURL rdf:resource="https://zenodo.org/record/3668497/files/CCMetagen-1.0.0.zip"/> <dcat:mediaType>application/zip</dcat:mediaType> </dcat:Distribution> </dcat:distribution> </rdf:Description> </rdf:RDF>
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