{"id":"https://openalex.org/W2901306713","doi":"https://doi.org/10.1186/s12859-018-2384-y","title":"TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms","display_name":"TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms","publication_year":2018,"publication_date":"2018-11-01","ids":{"openalex":"https://openalex.org/W2901306713","doi":"https://doi.org/10.1186/s12859-018-2384-y","mag":"2901306713","pmid":"https://pubmed.ncbi.nlm.nih.gov/30453874"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2384-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2384-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2384-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2384-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038138862","display_name":"Pedro Seoane","orcid":"https://orcid.org/0000-0002-3020-1415"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro Seoane","raw_affiliation_strings":["Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047344571","display_name":"Marina Espigares","orcid":null},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marina Espigares","raw_affiliation_strings":["Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088804009","display_name":"Rosario Carmona","orcid":"https://orcid.org/0000-0002-4235-2886"},"institutions":[{"id":"https://openalex.org/I4210092123","display_name":"Estaci\u00f3n Experimental del Zaid\u00edn","ror":"https://ror.org/00drcz023","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210092123"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rosario Carmona","raw_affiliation_strings":["Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estaci\u00f3n Experimental del Zaid\u00edn. CSIC, Prof. Albareda, 1, Granada, 18160, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estaci\u00f3n Experimental del Zaid\u00edn. CSIC, Prof. Albareda, 1, Granada, 18160, Spain","institution_ids":["https://openalex.org/I4210092123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047171856","display_name":"\u00c1lvaro Polonio","orcid":"https://orcid.org/0000-0002-4977-9305"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210137448","display_name":"Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\"","ror":"https://ror.org/04nrv3s86","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210137448","https://openalex.org/I82767444"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"\u00c1lvaro Polonio","raw_affiliation_strings":["Departamento de Microbiolog\u00eda, and Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\", Universidad de M\u00e1laga, Consejo Superior de Investigaciones Cient\u00edficas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Microbiolog\u00eda, and Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\", Universidad de M\u00e1laga, Consejo Superior de Investigaciones Cient\u00edficas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210137448","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037042657","display_name":"Julia Quintana","orcid":"https://orcid.org/0000-0002-5145-3590"},"institutions":[{"id":"https://openalex.org/I107077323","display_name":"Worcester Polytechnic Institute","ror":"https://ror.org/05ejpqr48","country_code":"US","type":"education","lineage":["https://openalex.org/I107077323"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julia Quintana","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280, USA","institution_ids":["https://openalex.org/I107077323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084018754","display_name":"Enrico Cretazzo","orcid":"https://orcid.org/0000-0001-7216-8441"},"institutions":[{"id":"https://openalex.org/I4210129002","display_name":"Andalusian Institute of Agricultural and Fisheries Research and Training","ror":"https://ror.org/02w21g732","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210129002","https://openalex.org/I918821925"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Enrico Cretazzo","raw_affiliation_strings":["Instituto Andaluz de Investigaci\u00f3n y Formaci\u00f3n Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto Andaluz de Investigaci\u00f3n y Formaci\u00f3n Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140, Spain","institution_ids":["https://openalex.org/I4210129002"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058076670","display_name":"Josefina Bota","orcid":"https://orcid.org/0000-0001-7039-7638"},"institutions":[{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Josefina Bota","raw_affiliation_strings":["Grup de Recerca en Biologia de les Plantes en Condicions Mediterr\u00e0nies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Biologia de les Plantes en Condicions Mediterr\u00e0nies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122, Spain","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066993860","display_name":"Alejandro P\u00e9rez\u2010Garc\u00eda","orcid":"https://orcid.org/0000-0002-1065-0360"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210137448","display_name":"Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\"","ror":"https://ror.org/04nrv3s86","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210137448","https://openalex.org/I82767444"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alejandro P\u00e9rez-Garc\u00eda","raw_affiliation_strings":["Departamento de Microbiolog\u00eda, and Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\", Universidad de M\u00e1laga, Consejo Superior de Investigaciones Cient\u00edficas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Microbiolog\u00eda, and Instituto de Hortofruticultura Subtropical y Mediterr\u00e1nea \"La Mayora\", Universidad de M\u00e1laga, Consejo Superior de Investigaciones Cient\u00edficas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210137448","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035114387","display_name":"Juan de Dios Alch\u00e9 Ram\u00edrez","orcid":"https://orcid.org/0000-0002-7547-6025"},"institutions":[{"id":"https://openalex.org/I4210092123","display_name":"Estaci\u00f3n Experimental del Zaid\u00edn","ror":"https://ror.org/00drcz023","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210092123"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan de Dios Alch\u00e9","raw_affiliation_strings":["Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estaci\u00f3n Experimental del Zaid\u00edn. CSIC, Prof. Albareda, 1, Granada, 18160, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estaci\u00f3n Experimental del Zaid\u00edn. CSIC, Prof. Albareda, 1, Granada, 18160, Spain","institution_ids":["https://openalex.org/I4210092123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031514818","display_name":"Luis G\u00f3mez","orcid":"https://orcid.org/0000-0002-4346-4820"},"institutions":[{"id":"https://openalex.org/I4210162265","display_name":"Centre for Plant Biotechnology and Genomics","ror":"https://ror.org/04mfzb702","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210162265"]},{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Luis G\u00f3mez","raw_affiliation_strings":["CBGP, INIA-Universidad Polit\u00e9cnica de Madrid, Campus de Montegancedo, Pozuelo de Alarc\u00f3n, 28223, Spain","Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Polit\u00e9cnica de Madrid, Ciudad Universitaria, Madrid, 28040, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CBGP, INIA-Universidad Polit\u00e9cnica de Madrid, Campus de Montegancedo, Pozuelo de Alarc\u00f3n, 28223, Spain","institution_ids":["https://openalex.org/I4210162265"]},{"raw_affiliation_string":"Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Polit\u00e9cnica de Madrid, Ciudad Universitaria, Madrid, 28040, Spain","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056017872","display_name":"M. Gonzalo Claros","orcid":"https://orcid.org/0000-0002-0112-3550"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"M. Gonzalo Claros","raw_affiliation_strings":["Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain. claros@uma.es","Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain. claros@uma.es","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Departmento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, Campus de Teatinos s/n, Malaga, 29071, Spain","institution_ids":["https://openalex.org/I82767444"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5056017872"],"corresponding_institution_ids":["https://openalex.org/I82767444"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6599,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.67575352,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"S14","first_page":"416","last_page":"416"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3878999948501587,"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":0.3878999948501587,"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/T11927","display_name":"Plant Reproductive Biology","score":0.10000000149011612,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.07680000364780426,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/de-novo-transcriptome-assembly","display_name":"De novo transcriptome assembly","score":0.7349585294723511},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6817418932914734},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6136718988418579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5877395272254944},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4928460121154785},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4298507273197174},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4119079113006592},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25356635451316833},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19156518578529358}],"concepts":[{"id":"https://openalex.org/C50489715","wikidata":"https://www.wikidata.org/wiki/Q5244960","display_name":"De novo transcriptome assembly","level":5,"score":0.7349585294723511},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6817418932914734},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6136718988418579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5877395272254944},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4928460121154785},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4298507273197174},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4119079113006592},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25356635451316833},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19156518578529358},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1186/s12859-018-2384-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2384-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2384-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30453874","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30453874","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:eciencia.urjc.es:10115/27136","is_oa":true,"landing_page_url":"https://hdl.handle.net/10115/27136","pdf_url":"https://eciencia.urjc.es/bitstream/10115/27136/1/2018_Seoane%20et%20al-BMC%20Bioinf.pdf","source":{"id":"https://openalex.org/S4377196484","display_name":"BURJC Digital (King Juan Carlos University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I182083151","host_organization_name":"Universidad Rey Juan Carlos","host_organization_lineage":["https://openalex.org/I182083151"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.repositoriosalud.es:10668/13208","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245506/pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4377196114","display_name":"RISalud Institutional Health Repository of Andaluc\u00eda","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:digital.csic.es:10261/172650","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/172650","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:doaj.org/article:2459d4873f294f74ab85d064b04998fe","is_oa":false,"landing_page_url":"https://doaj.org/article/2459d4873f294f74ab85d064b04998fe","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S14, Pp 97-114 (2018)","raw_type":"article"},{"id":"pmh:oai:eciencia.urjc.es:10115/29253","is_oa":true,"landing_page_url":"https://hdl.handle.net/10115/29253","pdf_url":null,"source":{"id":"https://openalex.org/S4377196484","display_name":"BURJC Digital (King Juan Carlos University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I182083151","host_organization_name":"Universidad Rey Juan Carlos","host_organization_lineage":["https://openalex.org/I182083151"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:5218640","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6245506","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:riuma.uma.es:10630/29258","is_oa":true,"landing_page_url":"https://hdl.handle.net/10630/29258","pdf_url":null,"source":{"id":"https://openalex.org/S4306401385","display_name":"Repositorio Institucional de la Universidad de M\u00e1laga (University of M\u00e1laga)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I82767444","host_organization_name":"Universidad de M\u00e1laga","host_organization_lineage":["https://openalex.org/I82767444"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2384-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2384-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2384-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1199208145","display_name":null,"funder_award_id":"201540E065","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G1888088267","display_name":null,"funder_award_id":"2014-2020\u2019","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1953887145","display_name":null,"funder_award_id":"2014\u20102020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2839268836","display_name":null,"funder_award_id":"AGL2016-76216-C2-1-R","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3715349637","display_name":null,"funder_award_id":"P10-CVI-6075","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G415846204","display_name":null,"funder_award_id":"AGL2013-41939-R","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4512531661","display_name":null,"funder_award_id":"AGL2016","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4875165668","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G5304379238","display_name":null,"funder_award_id":"RTC-2015-4181-2","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5520346886","display_name":null,"funder_award_id":"P2011-CVI-7487","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G6803900945","display_name":null,"funder_award_id":"BFU-2016-77243-P","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G707947270","display_name":null,"funder_award_id":"P2011-CVI7487","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G872876474","display_name":null,"funder_award_id":"RTC2016-4824-2","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320309969","display_name":"Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria","ror":"https://ror.org/011q66e29"},{"id":"https://openalex.org/F4320311265","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2901306713.pdf","grobid_xml":"https://content.openalex.org/works/W2901306713.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1550594300","https://openalex.org/W1554142489","https://openalex.org/W1786214811","https://openalex.org/W1970335548","https://openalex.org/W1971899779","https://openalex.org/W1987545661","https://openalex.org/W1994145712","https://openalex.org/W2033292629","https://openalex.org/W2033531015","https://openalex.org/W2040151959","https://openalex.org/W2059598891","https://openalex.org/W2069189895","https://openalex.org/W2077692176","https://openalex.org/W2110392562","https://openalex.org/W2112252734","https://openalex.org/W2112343742","https://openalex.org/W2112888168","https://openalex.org/W2118058166","https://openalex.org/W2120457919","https://openalex.org/W2126419817","https://openalex.org/W2127059936","https://openalex.org/W2136651963","https://openalex.org/W2153947402","https://openalex.org/W2155628349","https://openalex.org/W2156125289","https://openalex.org/W2156841387","https://openalex.org/W2166265186","https://openalex.org/W2173022995","https://openalex.org/W2236822143","https://openalex.org/W2308074142","https://openalex.org/W2331687108","https://openalex.org/W2460532444","https://openalex.org/W2463643813","https://openalex.org/W2510214295","https://openalex.org/W2528312975","https://openalex.org/W2551033818","https://openalex.org/W2559011563","https://openalex.org/W2949444664"],"related_works":["https://openalex.org/W4317780692","https://openalex.org/W4252248862","https://openalex.org/W4244502392","https://openalex.org/W4246813243","https://openalex.org/W3091263951","https://openalex.org/W1021674602","https://openalex.org/W2581777896","https://openalex.org/W2733793436","https://openalex.org/W4311517665","https://openalex.org/W2774392350"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"advances":[2],"in":[3,63,195],"high-throughput":[4],"sequencing":[5,115,123],"technologies":[6],"are":[7,44,127],"allowing":[8],"more":[9,11],"and":[10,25,33,42,74,113,117,137,151,154,161,171,255,270,274,290,306,313,319],"de":[12,60,184],"novo":[13,61,185],"assembling":[14,57,139,229],"of":[15,23,36,56,102,111,132,192,207,218,243,253,285,296],"transcriptomes":[16,62,136,141,173],"from":[17],"many":[18],"new":[19],"organisms.":[20],"Some":[21],"degree":[22],"automation":[24],"evaluation":[26,58,268],"is":[27,83,187,210],"required":[28],"to":[29,79,94,121,175,226,240,245],"warrant":[30],"reproducibility,":[31],"repetitivity":[32],"the":[34,37,54,100,103,130,138,165,177,205,279,328],"selection":[35,131],"best":[38,178,280],"possible":[39],"transcriptome.":[40],"Workflows":[41],"pipelines":[43],"becoming":[45],"an":[46,272],"absolute":[47],"requirement":[48],"for":[49,59,145,157,164,250,277,303,311],"such":[50],"a":[51,66,216,247,258,283],"purpose,":[52],"but":[53],"issue":[55],"organisms":[64],"lacking":[65],"sequenced":[67],"genome":[68],"remains":[69],"unsolved.":[70],"An":[71],"automated,":[72],"reproducible":[73],"flexible":[75],"framework":[76],"called":[77],"TransFlow":[78,86,222],"accomplish":[80],"this":[81],"task":[82],"described.":[84],"RESULTS:":[85],"with":[87,129,198,309,317,322],"its":[88,238,264],"five":[89],"independent":[90],"modules":[91],"was":[92],"designed":[93],"build":[95],"different":[96,109,228,241],"workflows":[97],"depending":[98],"on":[99,233],"nature":[101],"original":[104],"reads.":[105],"This":[106],"architecture":[107],"enables":[108],"combinations":[110],"Illumina":[112,189],"Roche/454":[114,323],"data,":[116],"can":[118,200,223],"be":[119,176],"extended":[120],"other":[122,155],"platforms.":[124],"Its":[125],"capabilities":[126],"illustrated":[128],"reliable":[133,202],"plant":[134],"reference":[135],"six":[140],"(three":[142],"case":[143,261],"studies":[144],"grapevine":[146],"leaves,":[147],"olive":[148],"tree":[149],"pollen,":[150],"chestnut":[152],"stem,":[153],"three":[156],"haustorium,":[158],"epiphytic":[159],"structures":[160],"their":[162],"combination":[163,252],"phytopathogenic":[166],"fungus":[167],"Podosphaera":[168],"xanthii).":[169],"Arabidopsis":[170],"poplar":[172],"revealed":[174],"references.":[179],"A":[180],"common":[181],"result":[182],"regarding":[183],"assemblies":[186],"that":[188],"paired-end":[190],"reads":[191,209,244,254],"100":[193],"nt":[194,298],"length":[196],"assembled":[197],"OASES":[199],"provide":[201,246],"transcriptomes,":[203],"while":[204],"contribution":[206],"longer":[208],"noticeable":[211],"only":[212],"when":[213,324],"they":[214],"complement":[215],"set":[217],"short,":[219],"single-reads.":[220],"CONCLUSIONS:":[221],"handle":[224],"up":[225],"181":[227],"strategies.":[230],"Evaluation":[231],"based":[232],"principal":[234],"component":[235],"analyses":[236],"allows":[237],"self-adaptation":[239],"sets":[242],"suitable":[248],"transcriptome":[249,281],"each":[251,260],"assemblers.":[256],"As":[257],"result,":[259],"study":[262],"has":[263],"own":[265],"behaviour,":[266],"prioritises":[267],"parameters,":[269],"gives":[271],"objective":[273],"automated":[275],"way":[276],"detecting":[278],"within":[282],"pool":[284],"them.":[286],"Sequencing":[287],"data":[288],"type":[289],"quantity":[291],"(preferably":[292,315],"several":[293],"hundred":[294],"millions":[295],"2\u00d7100":[297],"or":[299],"longer),":[300],"assemblers":[301],"(OASES":[302],"Illumina,":[304],"MIRA4":[305],"EULER-SR":[307],"reconciled":[308],"CAP3":[310],"Roche/454)":[312],"strategy":[314],"scaffolding":[316],"OASES,":[318],"probably":[320],"merging":[321],"available)":[325],"arise":[326],"as":[327],"most":[329],"impacting":[330],"factors.":[331]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
