{"id":"https://openalex.org/W7225115405","doi":"https://doi.org/10.5281/zenodo.23899195","title":"d\u0101naSeq mag_analysis: recovery, annotation and exploration of metagenome-assembled genomes","display_name":"d\u0101naSeq mag_analysis: recovery, annotation and exploration of metagenome-assembled genomes","publication_year":2026,"publication_date":"2026-11-02","ids":{"openalex":"https://openalex.org/W7225115405","doi":"https://doi.org/10.5281/zenodo.23899195"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.23899195","doi":"https://doi.org/10.5281/zenodo.23899195","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23899195","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"volume":null,"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.23899195","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054521581","display_name":"R. Eric Collins","orcid":"https://orcid.org/0000-0002-5858-2395","observed_orcids":["https://orcid.org/0000-0002-5858-2395"]},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Collins, R. Eric","raw_affiliation_strings":["University of Manitoba"],"raw_orcid":"https://orcid.org/0000-0002-5858-2395","affiliations":[{"raw_affiliation_string":"University of Manitoba","institution_ids":["https://openalex.org/I46247651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054521581"],"corresponding_institution_ids":["https://openalex.org/I46247651"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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":0.002099999925121665,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.0005000000237487257,"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/metagenome-assembled-genomes","display_name":"metagenome-assembled genomes","score":0.9980000257492065},{"id":"https://openalex.org/keywords/co-assembly","display_name":"co-assembly","score":0.6460000276565552},{"id":"https://openalex.org/keywords/nextflow-pipeline","display_name":"Nextflow pipeline","score":0.6669999957084656},{"id":"https://openalex.org/keywords/dereplication","display_name":"dereplication","score":0.703000009059906},{"id":"https://openalex.org/keywords/biosynthetic-gene-clusters","display_name":"biosynthetic gene clusters","score":0.9879999756813049},{"id":"https://openalex.org/keywords/mobile-genetic-elements","display_name":"mobile genetic elements","score":0.9629999995231628},{"id":"https://openalex.org/keywords/defense-systems","display_name":"defense systems","score":0.6060000061988831},{"id":"https://openalex.org/keywords/ecosystem-services","display_name":"ecosystem services","score":0.7310000061988831},{"id":"https://openalex.org/keywords/sustainable-development-goals","display_name":"Sustainable Development Goals","score":0.8870000243186951},{"id":"https://openalex.org/keywords/reproducible-analysis","display_name":"reproducible analysis","score":0.4490000009536743},{"id":"https://openalex.org/keywords/containerized-workflows","display_name":"containerized workflows","score":0.47200000286102295}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7181000113487244},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.710099995136261},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.6195999979972839},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5636000037193298},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5515999794006348},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5342000126838684},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5008000135421753},{"id":"https://openalex.org/C2781018962","wikidata":"https://www.wikidata.org/wiki/Q5164884","display_name":"Container (type theory)","level":2,"score":0.48069998621940613},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4772000014781952},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.4503999948501587},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4496000111103058},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.40389999747276306},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.3978999853134155},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3804999887943268},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35910001397132874},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.35850000381469727},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.3521000146865845},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.34779998660087585},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.32749998569488525},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.31869998574256897},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3131999969482422},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3100999891757965},{"id":"https://openalex.org/C174683762","wikidata":"https://www.wikidata.org/wiki/Q609588","display_name":"Component-based software engineering","level":4,"score":0.2865000069141388},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2833999991416931},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.272599995136261},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.2671999931335449},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.26589998602867126},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2639000117778778},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.26109999418258667},{"id":"https://openalex.org/C2776650193","wikidata":"https://www.wikidata.org/wiki/Q264661","display_name":"Obstacle","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.2540999948978424},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.25060001015663147}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.23899195","doi":"https://doi.org/10.5281/zenodo.23899195","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23899195","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.5281/zenodo.23899196","doi":"https://doi.org/10.5281/zenodo.23899196","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23899196","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.5281/zenodo.23899195","doi":"https://doi.org/10.5281/zenodo.23899195","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23899195","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2952603008","https://openalex.org/W4282983820","https://openalex.org/W4225972470","https://openalex.org/W4322492213","https://openalex.org/W7090843276","https://openalex.org/W7152401230","https://openalex.org/W3217463608","https://openalex.org/W4306893447","https://openalex.org/W7225106466","https://openalex.org/W4414559152"],"abstract_inverted_index":{"Motivation:":[0],"Recovering":[1],"metagenome-assembled":[2],"genomes":[3],"(MAGs)":[4],"from":[5,68,181,185],"an":[6,60],"environmental":[7,43],"co-assembly":[8],"involves":[9],"many":[10,42],"tools":[11],"with":[12,72,99,103,110,117,173],"incompatible":[13],"input":[14],"formats,":[15],"conflicting":[16],"software":[17],"dependencies,":[18],"large":[19],"reference":[20],"databases":[21],"and":[22,33,63,89,105,107,121,136,143,148,156,167,187,219],"heterogeneous":[23],"hardware":[24],"requirements.":[25],"Running":[26],"them":[27],"reproducibly":[28],"on":[29,193],"shared":[30],"computing":[31],"systems,":[32,145],"inspecting":[34],"the":[35,49,54,122,179,207,225],"results,":[36],"is":[37,48,114,222],"a":[38,64,169,194,198,211],"practical":[39],"obstacle":[40],"for":[41],"microbiology":[44],"groups.":[45],"Results:":[46],"mag_analysis":[47],"downstream":[50],"Nextflow":[51],"pipeline":[52,180],"of":[53,151],"d\u0101naSeq":[55,221],"suite.":[56],"Its":[57],"inputs":[58],"are":[59,124,162,204],"assembly":[61,113],"FASTA":[62],"MetaBAT2-format":[65],"depth":[66],"table":[67],"any":[69],"assembler,":[70],"optionally":[71,101],"sorted":[73],"BAM":[74],"files.":[75],"It":[76],"runs":[77,178],"up":[78],"to":[79,126,233],"seven":[80],"binners":[81],"(SemiBin2,":[82],"MetaBAT2,":[83],"MaxBin2,":[84],"LorBin,":[85],"COMEBin,":[86],"VAMB,":[87],"TaxVAMB)":[88],"three":[90],"consensus":[91],"methods":[92],"(DAS":[93],"Tool,":[94],"Binette,":[95],"MAGScoT),":[96],"estimates":[97],"quality":[98],"CheckM2,":[100],"dereplicates":[102],"galah":[104],"skani,":[106],"places":[108],"bins":[109],"GTDB-Tk.":[111],"The":[112],"annotated":[115],"once":[116],"Bakta":[118],"or":[119,184,196],"Prokka":[120],"annotations":[123],"mapped":[125],"bins.":[127],"Optional":[128],"modules":[129],"cover":[130],"contig":[131],"taxonomy,":[132],"rRNA":[133],"genes,":[134],"metabolism":[135],"biosynthetic":[137],"gene":[138],"clusters,":[139],"mobile":[140],"genetic":[141],"elements":[142],"defence":[144],"eukaryotic":[146],"contigs,":[147],"ECOSSDB":[149],"scoring":[150],"CICES":[152],"5.2":[153],"ecosystem":[154],"services":[155],"UN":[157],"Sustainable":[158],"Development":[159],"Goals.":[160],"Results":[161],"written":[163],"as":[164,168],"per-analysis":[165],"tables":[166],"static":[170],"web":[171],"dashboard":[172],"eleven":[174],"views.":[175],"A":[176],"launcher":[177],"conda":[182],"environments":[183],"CPU":[186],"CUDA":[188],"container":[189],"images":[190],"(Docker,":[191],"Apptainer/Singularity),":[192],"workstation":[195],"inside":[197],"single":[199],"Slurm":[200],"allocation.":[201],"Finished":[202],"stages":[203],"kept":[205],"in":[206],"output":[208],"directory,":[209],"so":[210],"resubmitted":[212],"job":[213],"resumes":[214],"where":[215],"it":[216],"stopped.":[217],"Availability":[218],"implementation:":[220],"released":[223],"under":[224],"MIT":[226],"license":[227],"at":[228,238],"https://github.com/rec3141/danaSeq":[229],"(this":[230],"description":[231],"corresponds":[232],"release":[234],"v1.3.0,":[235],"https://github.com/rec3141/danaSeq/releases/tag/v1.3.0);":[236],"documentation":[237],"https://rec3141.github.io/danaSeq/.":[239]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-11-03T00:00:00"}
