{"id":"https://openalex.org/W2136264360","doi":"https://doi.org/10.1093/bioinformatics/btu661","title":"A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data","display_name":"A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data","publication_year":2014,"publication_date":"2014-10-22","ids":{"openalex":"https://openalex.org/W2136264360","doi":"https://doi.org/10.1093/bioinformatics/btu661","mag":"2136264360","pmid":"https://pubmed.ncbi.nlm.nih.gov/25338718"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/587/49011019/bioinformatics_31_4_587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/587/49011019/bioinformatics_31_4_587.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028399086","display_name":"David A. Coil","orcid":"https://orcid.org/0000-0001-6049-8240"},"institutions":[{"id":"https://openalex.org/I114017466","display_name":"University of Technology Sydney","ror":"https://ror.org/03f0f6041","country_code":"AU","type":"education","lineage":["https://openalex.org/I114017466"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["AU","US"],"is_corresponding":true,"raw_author_name":"David Coil","raw_affiliation_strings":["1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"],"affiliations":[{"raw_affiliation_string":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia","institution_ids":["https://openalex.org/I84218800","https://openalex.org/I114017466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086222406","display_name":"Guillaume Jospin","orcid":"https://orcid.org/0000-0002-8746-2632"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]},{"id":"https://openalex.org/I114017466","display_name":"University of Technology Sydney","ror":"https://ror.org/03f0f6041","country_code":"AU","type":"education","lineage":["https://openalex.org/I114017466"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Guillaume Jospin","raw_affiliation_strings":["1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"],"affiliations":[{"raw_affiliation_string":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia","institution_ids":["https://openalex.org/I84218800","https://openalex.org/I114017466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047169338","display_name":"Aaron E. Darling","orcid":"https://orcid.org/0000-0003-2397-7925"},"institutions":[{"id":"https://openalex.org/I114017466","display_name":"University of Technology Sydney","ror":"https://ror.org/03f0f6041","country_code":"AU","type":"education","lineage":["https://openalex.org/I114017466"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Aaron E. Darling","raw_affiliation_strings":["1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"],"affiliations":[{"raw_affiliation_string":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia","institution_ids":["https://openalex.org/I84218800","https://openalex.org/I114017466"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028399086"],"corresponding_institution_ids":["https://openalex.org/I114017466","https://openalex.org/I84218800"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":33.4545,"has_fulltext":true,"cited_by_count":1158,"citation_normalized_percentile":{"value":0.99876176,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"31","issue":"4","first_page":"587","last_page":"589"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9632999897003174,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9631999731063843,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/adapter","display_name":"Adapter (computing)","score":0.7568252086639404},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7231322526931763},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6035081148147583},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.5458917021751404},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4995267391204834},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4751529395580292},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4468718469142914},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.43974101543426514},{"id":"https://openalex.org/keywords/trimming","display_name":"Trimming","score":0.43491876125335693},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36848580837249756},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25839197635650635},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18638426065444946},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15102803707122803},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13871410489082336}],"concepts":[{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.7568252086639404},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7231322526931763},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6035081148147583},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.5458917021751404},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4995267391204834},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4751529395580292},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4468718469142914},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.43974101543426514},{"id":"https://openalex.org/C56951928","wikidata":"https://www.wikidata.org/wiki/Q3539213","display_name":"Trimming","level":2,"score":0.43491876125335693},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36848580837249756},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25839197635650635},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18638426065444946},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15102803707122803},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13871410489082336}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/587/49011019/bioinformatics_31_4_587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25338718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25338718","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/587/49011019/bioinformatics_31_4_587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332946","display_name":"NSW Department of Primary Industries","ror":"https://ror.org/050khh066"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136264360.pdf","grobid_xml":"https://content.openalex.org/works/W2136264360.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1998258963","https://openalex.org/W2107772251","https://openalex.org/W2115501618","https://openalex.org/W2120902911","https://openalex.org/W2127781493","https://openalex.org/W2141920662","https://openalex.org/W2146728635"],"related_works":["https://openalex.org/W2467235537","https://openalex.org/W4243755427","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535","https://openalex.org/W3123068371","https://openalex.org/W2479811461","https://openalex.org/W2104915799","https://openalex.org/W2355429491"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":89},{"year":2024,"cited_by_count":106},{"year":2023,"cited_by_count":91},{"year":2022,"cited_by_count":102},{"year":2021,"cited_by_count":146},{"year":2020,"cited_by_count":124},{"year":2019,"cited_by_count":140},{"year":2018,"cited_by_count":108},{"year":2017,"cited_by_count":104},{"year":2016,"cited_by_count":84},{"year":2015,"cited_by_count":43},{"year":2014,"cited_by_count":4}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}