{"id":"https://openalex.org/W7212318563","doi":"https://doi.org/10.64898/2026.09.05.749574","title":"Geomosaic: a flexible bioinformatics platform integrating complementary metagenomic analyses from sequencing reads to genomes","display_name":"Geomosaic: a flexible bioinformatics platform integrating complementary metagenomic analyses from sequencing reads to genomes","publication_year":2026,"publication_date":"2026-09-11","ids":{"openalex":"https://openalex.org/W7212318563","doi":"https://doi.org/10.64898/2026.09.05.749574"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.05.749574","doi":"https://doi.org/10.64898/2026.09.05.749574","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.05.749574","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.05.749574.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.05.749574.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079075510","display_name":"Davide Corso","orcid":"https://orcid.org/0000-0001-8845-3693","observed_orcids":["https://orcid.org/0000-0001-8845-3693"]},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Corso","raw_affiliation_strings":["Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8845-3693","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117484481","display_name":"Edoardo Taccaliti","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Edoardo Taccaliti","raw_affiliation_strings":["Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017192565","display_name":"Bernardo Barosa","orcid":"https://orcid.org/0009-0002-9779-3571","observed_orcids":["https://orcid.org/0009-0002-9779-3571"]},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Bernardo Barosa","raw_affiliation_strings":["Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089320122","display_name":"Donato Giovannelli","orcid":"https://orcid.org/0000-0001-7182-8233","observed_orcids":["https://orcid.org/0000-0001-7182-8233"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698","https://openalex.org/I4400009020"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4387154004","display_name":"Institute for Marine Biological Resources and Biotechnology","ror":"https://ror.org/00pb0ac76","country_code":"IT","type":"other","lineage":["https://openalex.org/I4210155236","https://openalex.org/I4387154004"]},{"id":"https://openalex.org/I4387156061","display_name":"Earth-Life Science Institute","ror":"https://ror.org/031dp5151","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4387156061","https://openalex.org/I4400009020","https://openalex.org/I4405286867"]},{"id":"https://openalex.org/I66958751","display_name":"Woods Hole Oceanographic Institution","ror":"https://ror.org/03zbnzt98","country_code":"US","type":"funder","lineage":["https://openalex.org/I66958751"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT","JP","US"],"is_corresponding":true,"raw_author_name":"Donato Giovannelli","raw_affiliation_strings":["Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy","Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA","Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan","Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale delle Ricerche, CNR-IRBIM, Ancona, Italy","Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-7182-8233","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Naples \u201cFederico II\u201d, Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698","https://openalex.org/I4387156061"]},{"raw_affiliation_string":"Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale delle Ricerche, CNR-IRBIM, Ancona, Italy","institution_ids":["https://openalex.org/I4210155236","https://openalex.org/I4387154004"]},{"raw_affiliation_string":"Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA","institution_ids":["https://openalex.org/I66958751"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5089320122"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I114531698","https://openalex.org/I4210155236","https://openalex.org/I4387154004","https://openalex.org/I4387156061","https://openalex.org/I66958751","https://openalex.org/I71267560"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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":0.9955999851226807,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0010999999940395355,"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"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.7670000195503235},{"id":"https://openalex.org/keywords/genome-resolved-metagenomics","display_name":"genome-resolved metagenomics","score":0.8820000290870667},{"id":"https://openalex.org/keywords/metagenomic-assembly","display_name":"metagenome assembly","score":0.7860000133514404},{"id":"https://openalex.org/keywords/snakemake","display_name":"Snakemake","score":0.9020000100135803},{"id":"https://openalex.org/keywords/reproducible-analysis-workflow","display_name":"reproducible analysis workflow","score":0.5479999780654907},{"id":"https://openalex.org/keywords/taxonomic-profiling","display_name":"taxonomic profiling","score":0.7419999837875366},{"id":"https://openalex.org/keywords/functional-profiling","display_name":"functional profiling","score":0.9620000123977661},{"id":"https://openalex.org/keywords/genome-reconstruction","display_name":"genome reconstruction","score":0.5649999976158142},{"id":"https://openalex.org/keywords/hpc","display_name":"HPC","score":0.3449999988079071},{"id":"https://openalex.org/keywords/environmental-metagenomics","display_name":"environmental metagenomics","score":0.8360000252723694}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9253000020980835},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.839900016784668},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7537999749183655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7243000268936157},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5529000163078308},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5105999708175659},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4902999997138977},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48260000348091125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42800000309944153},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.38760000467300415},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.34599998593330383},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3441999852657318},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.301800012588501},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.28209999203681946},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2533999979496002}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.05.749574","doi":"https://doi.org/10.64898/2026.09.05.749574","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.05.749574","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.05.749574.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.05.749574","doi":"https://doi.org/10.64898/2026.09.05.749574","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.05.749574","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.05.749574.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6752308677","display_name":null,"funder_award_id":"948972","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212318563.pdf","grobid_xml":"https://content.openalex.org/works/W7212318563.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1596936080","https://openalex.org/W1878521557","https://openalex.org/W2107772251","https://openalex.org/W2112364185","https://openalex.org/W2113679889","https://openalex.org/W2115026474","https://openalex.org/W2124985265","https://openalex.org/W2131271579","https://openalex.org/W2138122982","https://openalex.org/W2143485490","https://openalex.org/W2152722971","https://openalex.org/W2337747100","https://openalex.org/W2419548415","https://openalex.org/W2599417231","https://openalex.org/W2611147605","https://openalex.org/W2753961085","https://openalex.org/W2798209956","https://openalex.org/W2938868597","https://openalex.org/W2950464960","https://openalex.org/W2950785362","https://openalex.org/W2951220983","https://openalex.org/W2990618091","https://openalex.org/W2991239467","https://openalex.org/W3048272826","https://openalex.org/W3094445727","https://openalex.org/W3125972683","https://openalex.org/W3128393598","https://openalex.org/W3203343200","https://openalex.org/W3209528471","https://openalex.org/W4224257212","https://openalex.org/W4225007447","https://openalex.org/W4281868629","https://openalex.org/W4285060784","https://openalex.org/W4304481015","https://openalex.org/W4306698396","https://openalex.org/W4321611856","https://openalex.org/W4375863320","https://openalex.org/W4386027910","https://openalex.org/W4402253358","https://openalex.org/W4406226166","https://openalex.org/W6892440325","https://openalex.org/W6912636611","https://openalex.org/W6930033015","https://openalex.org/W7133302540"],"related_works":["https://openalex.org/W4362736020","https://openalex.org/W2145044321","https://openalex.org/W4412492460","https://openalex.org/W4415887721","https://openalex.org/W4414764907","https://openalex.org/W4416535827","https://openalex.org/W6926441655","https://openalex.org/W1976855715","https://openalex.org/W4220739086","https://openalex.org/W4401345507"],"abstract_inverted_index":{"ABSTRACT":[0,247],"Metagenomic":[1],"analyses":[2,149,237,256,275,291],"can":[3],"be":[4],"performed":[5],"at":[6],"multiple":[7,138],"analytical":[8,24,37,62,98,192],"levels,":[9],"including":[10],"read-based,":[11],"assembly-based,":[12],"and":[13,26,76,114,125,137,158,187,213,226,238,243,253,260,270,288,307,314,320,326],"genome-resolved":[14,120,188,254,280,289],"approaches,":[15],"each":[16],"capturing":[17],"complementary":[18,45,61,198,250],"biological":[19,203],"information":[20],"while":[21,100,154],"introducing":[22],"distinct":[23],"biases":[25],"trade-offs.":[27],"However,":[28],"existing":[29],"workflows":[30,94],"are":[31],"commonly":[32],"optimized":[33],"for":[34,150,166,234],"a":[35,48,56,72,81,231,258,293],"single":[36,73,294],"strategy,":[38],"making":[39],"it":[40],"difficult":[41],"to":[42,69,90,145,178,207,279],"integrate":[43],"these":[44],"representations":[46,63,199],"within":[47,71,257],"unified,":[49],"reproducible":[50,77,240],"framework.":[51],"Here":[52],"we":[53],"present":[54],"Geomosaic,":[55],"modular":[57,135,259,295,305],"framework":[58,107],"that":[59],"integrates":[60,195,249,285],"of":[64,132,172,200,334],"metagenomic":[65,148,180,236,255,274,290,335],"data,":[66],"from":[67,175,276],"reads":[68],"genomes,":[70],"scalable,":[74],"customizable,":[75],"workflow.":[78,262],"Built":[79],"on":[80],"graph-based":[82,299],"architecture":[83,265,300],"implemented":[84],"in":[85,292],"Snakemake,":[86],"Geomosaic":[87,143,194,229,248,284],"enables":[88,169,301],"users":[89,206],"construct":[91],"complete":[92],"end-to-end":[93],"or":[95],"execute":[96],"individual":[97,176],"modules":[99],"selecting":[101],"among":[102],"interchangeable":[103],"software":[104],"packages.":[105],"The":[106],"supports":[108],"read":[109],"preprocessing,":[110],"quality":[111],"control,":[112],"taxonomic":[113],"functional":[115,215,336],"profiling,":[116],"assembly,":[117],"genome":[118],"reconstruction,":[119],"annotation,":[121],"custom":[122],"HMM-based":[123],"analyses,":[124],"automated":[126],"downstream":[127,241],"result":[128],"aggregation.":[129],"Automatic":[130],"generation":[131,313],"execution":[133],"scripts,":[134],"workflows,":[136],"analysis":[139,171],"entry":[140],"points":[141],"make":[142],"accessible":[144],"researchers":[146],"approaching":[147],"the":[151,156,201],"first":[152],"time,":[153],"providing":[155],"flexibility":[157],"control":[159],"required":[160],"by":[161],"expert":[162,321],"users.":[163,322],"Native":[164],"support":[165,317],"HPC":[167],"environments":[168],"efficient":[170],"datasets":[173],"ranging":[174],"projects":[177],"large-scale":[179],"surveys.":[181],"Rather":[182],"than":[183],"treating":[184],"read-,":[185,251,286],"assembly-,":[186,252,287],"metagenomics":[189],"as":[190,197],"alternative":[191],"strategies,":[193],"them":[196],"same":[202],"system,":[204],"allowing":[205],"move":[208],"seamlessly":[209],"between":[210],"community-wide":[211,277],"patterns":[212],"organism-resolved":[214],"interpretation.":[216],"By":[217],"combining":[218],"workflow":[219,312],"flexibility,":[220],"computational":[221],"reproducibility,":[222],"standardized":[223],"analysis-ready":[224],"outputs,":[225],"extensive":[227],"documentation,":[228],"provides":[230],"unified":[232],"platform":[233],"environmental":[235],"facilitates":[239],"ecological":[242,332],"evolutionary":[244],"investigations.":[245],"GRAPHICAL":[246],"scalable":[261],"Its":[263],"mosaic-like":[264],"combines":[266],"flexible":[267,302],"tool":[268,303],"selection":[269],"HPC-ready":[271,315],"execution,":[272,306],"supporting":[273],"profiling":[278],"characterization.":[281],"HIGHLIGHTS":[282],"-":[283,297,310,323],"platform.":[296],"A":[298],"selection,":[304],"extensible":[308],"workflows.":[309],"Automated":[311],"scripts":[316],"both":[318],"entry-level":[319],"Redox":[324],"Metabolic":[325],"Metal":[327],"Plasticity":[328],"Indexes":[329],"provide":[330],"additional":[331],"interpretation":[333],"potential.":[337]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-12T00:00:00"}
