{"id":"https://openalex.org/W2059019569","doi":"https://doi.org/10.1093/bib/bbr074","title":"Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies","display_name":"Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies","publication_year":2011,"publication_date":"2011-12-23","ids":{"openalex":"https://openalex.org/W2059019569","doi":"https://doi.org/10.1093/bib/bbr074","mag":"2059019569","pmid":"https://pubmed.ncbi.nlm.nih.gov/22199379"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr074","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr074","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/213/545590/bbr074.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/14/2/213/545590/bbr074.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058192453","display_name":"Michael C. Schatz","orcid":"https://orcid.org/0000-0002-4118-4446"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. C. Schatz","raw_affiliation_strings":["Cold Spring Harbor, New York, NY 11724, USA. mschatz@cshl.edu","Cold Spring Harbor, New York, NY 11724, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor, New York, NY 11724, USA. mschatz@cshl.edu","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor, New York, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086869042","display_name":"Adam M. Phillippy","orcid":"https://orcid.org/0000-0003-2983-8934"},"institutions":[{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A. M. Phillippy","raw_affiliation_strings":["Adam M. Phillippy, PhD is a Principal Investigator of Genomics and Bioinformatics at the National Biodefense Analysis and Countermeasures Center","National Biodefense Analysis and Countermeasures Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Adam M. Phillippy, PhD is a Principal Investigator of Genomics and Bioinformatics at the National Biodefense Analysis and Countermeasures Center","institution_ids":["https://openalex.org/I4210118410"]},{"raw_affiliation_string":"National Biodefense Analysis and Countermeasures Center","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008513219","display_name":"Doron D. Sommer","orcid":"https://orcid.org/0000-0001-9692-7414"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"D. D. Sommer","raw_affiliation_strings":["Daniel D. Sommer is a bioinformatics engineer in the Center for Bioinformatics and Computational Biology at the University of Maryland","University of Maryland, College Park"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daniel D. Sommer is a bioinformatics engineer in the Center for Bioinformatics and Computational Biology at the University of Maryland","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"University of Maryland, College Park","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085514105","display_name":"Arthur L. Delcher","orcid":null},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I165556055","display_name":"Loyola University Maryland","ror":"https://ror.org/01by1wp65","country_code":"US","type":"education","lineage":["https://openalex.org/I165556055"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. L. Delcher","raw_affiliation_strings":["Arthur L. Delcher, PhD is an Instructor at the Institute for Genome Sciences at the University of Maryland School of Medicine and Professor Emeritus of Computer Science at Loyola University Maryland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arthur L. Delcher, PhD is an Instructor at the Institute for Genome Sciences at the University of Maryland School of Medicine and Professor Emeritus of Computer Science at Loyola University Maryland","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I165556055"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036638042","display_name":"Daniela Puiu","orcid":"https://orcid.org/0000-0002-2386-9265"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Puiu","raw_affiliation_strings":["Daniela Puiu is a senior software engineer in the Institute of Genetic Medicine at Johns Hopkins University School of Medicine","Johns Hopkins University ("],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daniela Puiu is a senior software engineer in the Institute of Genetic Medicine at Johns Hopkins University School of Medicine","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Johns Hopkins University (","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081842800","display_name":"Giuseppe Narzisi","orcid":"https://orcid.org/0000-0003-1118-8849"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. Narzisi","raw_affiliation_strings":["Giuseppe Narzisi, PhD, is a Research Scientist at the NYU Bioinformatics Lab of Courant Institute of Mathematical Sciences after receiving a PhD in CS from NYU in May 2011","New York University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Giuseppe Narzisi, PhD, is a Research Scientist at the NYU Bioinformatics Lab of Courant Institute of Mathematical Sciences after receiving a PhD in CS from NYU in May 2011","institution_ids":["https://openalex.org/I36672615"]},{"raw_affiliation_string":"New York University","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010384159","display_name":"Steven L. Salzberg","orcid":"https://orcid.org/0000-0002-8859-7432"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. L. Salzberg","raw_affiliation_strings":["Steven L. Salzberg, PhD, is a Professor of Medicine and Biostatistics in the Institute of Genetic Medicine at Johns Hopkins University. From 2005 to 2011 he was Director of the Center for Bioinformatics and Computational Biology at the University of Maryland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Steven L. Salzberg, PhD, is a Professor of Medicine and Biostatistics in the Institute of Genetic Medicine at Johns Hopkins University. From 2005 to 2011 he was Director of the Center for Bioinformatics and Computational Biology at the University of Maryland","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064979917","display_name":"Mihai Pop","orcid":"https://orcid.org/0000-0001-9617-5304"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Pop","raw_affiliation_strings":["Mihai Pop, PhD, is an Associate Professor and Interim Director of the Center for Bioinformatics and Computational Biology at the University of Maryland","University of Maryland, College Park"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mihai Pop, PhD, is an Associate Professor and Interim Director of the Center for Bioinformatics and Computational Biology at the University of Maryland","institution_ids":[]},{"raw_affiliation_string":"University of Maryland, College Park","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5058192453"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2786,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.92754941,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"14","issue":"2","first_page":"213","last_page":"224"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9965999722480774,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.979200005531311,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/genome","display_name":"Genome","score":0.7106794714927673},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6603766679763794},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5254147052764893},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47943681478500366},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.47746920585632324},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.44675397872924805},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4283002018928528},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.4120527505874634},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3974176049232483},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.385293573141098},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2699527144432068},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20844948291778564},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.16455116868019104},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15405741333961487},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09581422805786133},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08115801215171814}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7106794714927673},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6603766679763794},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5254147052764893},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47943681478500366},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.47746920585632324},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.44675397872924805},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4283002018928528},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.4120527505874634},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3974176049232483},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.385293573141098},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2699527144432068},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20844948291778564},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.16455116868019104},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15405741333961487},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09581422805786133},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08115801215171814},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbr074","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr074","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/213/545590/bbr074.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22199379","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22199379","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:repository.cshl.edu:28335","is_oa":false,"landing_page_url":"http://repository.cshl.edu/id/eprint/28335/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Paper"},{"id":"pmh:oai:europepmc.org:2920662","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3603210","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3603210","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3603210","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr074","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr074","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/213/545590/bbr074.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1582564464","display_name":null,"funder_award_id":"R01 GM083873","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2415649048","display_name":null,"funder_award_id":"R01-HG004885","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G376875745","display_name":null,"funder_award_id":"R01-LM006845","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G552568885","display_name":null,"funder_award_id":"R01 HG006102","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7929101816","display_name":null,"funder_award_id":"R01 HG006677","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7951958147","display_name":null,"funder_award_id":"R01-HG006677","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2059019569.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1494075612","https://openalex.org/W1521810317","https://openalex.org/W1635391495","https://openalex.org/W1841715584","https://openalex.org/W1963524639","https://openalex.org/W1966822396","https://openalex.org/W1992950355","https://openalex.org/W2022986961","https://openalex.org/W2033083661","https://openalex.org/W2033531015","https://openalex.org/W2061069912","https://openalex.org/W2078331392","https://openalex.org/W2096634299","https://openalex.org/W2101021876","https://openalex.org/W2104146295","https://openalex.org/W2107282968","https://openalex.org/W2114765236","https://openalex.org/W2115521594","https://openalex.org/W2120414630","https://openalex.org/W2127230663","https://openalex.org/W2129873761","https://openalex.org/W2133956160","https://openalex.org/W2141217788","https://openalex.org/W2144662851","https://openalex.org/W2151464048","https://openalex.org/W2152073175","https://openalex.org/W2156622081","https://openalex.org/W2159497035","https://openalex.org/W2159946869","https://openalex.org/W2160770624","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2171531867","https://openalex.org/W2912500497","https://openalex.org/W3216020230"],"related_works":["https://openalex.org/W2148525144","https://openalex.org/W4234269430","https://openalex.org/W2066992345","https://openalex.org/W2582968398","https://openalex.org/W2181693928","https://openalex.org/W2765161871","https://openalex.org/W3209087738","https://openalex.org/W3012440071","https://openalex.org/W212334026","https://openalex.org/W4211093350"],"abstract_inverted_index":{"Since":[0],"its":[1],"launch":[2],"in":[3,65,102],"2004,":[4],"the":[5,25,30,39,47,97,117,133,140],"open-source":[6],"AMOS":[7,101,150],"project":[8],"has":[9],"released":[10],"several":[11],"innovative":[12],"DNA":[13],"sequence":[14],"analysis":[15],"applications":[16,53],"including:":[17],"Hawkeye,":[18],"a":[19,42,136],"visual":[20,118],"analytics":[21,119],"tool":[22],"for":[23,36,82,112,129],"inspecting":[24],"structure":[26,143],"of":[27,41,62,100,104,121,135],"genome":[28,43,50,137,142],"assemblies;":[29],"Assembly":[31],"Forensics":[32],"and":[33,45,59,90,116,131,149],"FRCurve":[34],"pipelines":[35],"systematically":[37],"evaluating":[38],"quality":[40,115],"assembly;":[44],"AMOScmp,":[46],"first":[48],"comparative":[49],"assembler.":[51],"These":[52,123],"have":[54,76],"been":[55,77],"used":[56],"to":[57,145],"assemble":[58],"analyze":[60],"dozens":[61],"genomes":[63],"ranging":[64],"complexity":[66],"from":[67,139],"simple":[68],"microbial":[69],"species":[70],"through":[71],"mammalian":[72],"genomes.":[73],"Recent":[74],"efforts":[75],"focused":[78],"on":[79,87,110],"enhancing":[80],"support":[81],"new":[83],"data":[84],"characteristics":[85],"brought":[86],"by":[88],"second-":[89],"now":[91],"third-generation":[92],"sequencing.":[93],"This":[94],"review":[95],"describes":[96],"major":[98],"components":[99],"light":[103],"these":[105],"challenges,":[106],"with":[107],"an":[108],"emphasis":[109],"methods":[111],"assessing":[113],"assembly":[114],"capabilities":[120],"Hawkeye.":[122],"interactive":[124],"graphical":[125],"aspects":[126],"are":[127,151],"essential":[128],"navigating":[130],"understanding":[132],"complexities":[134],"assembly,":[138],"overall":[141],"down":[144],"individual":[146],"bases.":[147],"Hawkeye":[148],"available":[152],"open":[153],"source":[154],"at":[155],"http://amos.sourceforge.net.":[156]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}