{"id":"https://openalex.org/W4283762274","doi":"https://doi.org/10.3389/fbinf.2022.893933","title":"Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2","display_name":"Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2","publication_year":2022,"publication_date":"2022-07-01","ids":{"openalex":"https://openalex.org/W4283762274","doi":"https://doi.org/10.3389/fbinf.2022.893933","pmid":"https://pubmed.ncbi.nlm.nih.gov/36304319"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2022.893933","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.893933","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/fbinf.2022.893933","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049385580","display_name":"Attayeb Mohsen","orcid":"https://orcid.org/0000-0003-0690-8012"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Attayeb Mohsen","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006097304","display_name":"Y. Ann Chen","orcid":"https://orcid.org/0000-0003-1468-3490"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yi-An Chen","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041859799","display_name":"Rodolfo S. Allendes Osorio","orcid":"https://orcid.org/0000-0002-9627-9338"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rodolfo S. Allendes Osorio","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020623644","display_name":"Chihiro Higuchi","orcid":"https://orcid.org/0000-0003-2808-2813"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Chihiro Higuchi","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061134485","display_name":"Kenji Mizuguchi","orcid":"https://orcid.org/0000-0003-3021-7078"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]},{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenji Mizuguchi","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","Institute for Protein Research, Osaka University, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]},{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049385580"],"corresponding_institution_ids":["https://openalex.org/I4210086383"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.772,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68633901,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"2","issue":null,"first_page":"893933","last_page":"893933"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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/T10066","display_name":"Gut microbiota and health","score":0.9976000189781189,"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":0.9957000017166138,"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/computer-science","display_name":"Computer science","score":0.81607985496521},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7735937833786011},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.7319061756134033},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5267224311828613},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5085707902908325},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5053406357765198},{"id":"https://openalex.org/keywords/confusion","display_name":"Confusion","score":0.4763769805431366},{"id":"https://openalex.org/keywords/installation","display_name":"Installation","score":0.45420002937316895},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4536033868789673},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.4260508418083191},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3240204453468323},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1423361599445343},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09076538681983948}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.81607985496521},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7735937833786011},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.7319061756134033},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5267224311828613},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5085707902908325},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5053406357765198},{"id":"https://openalex.org/C2781140086","wikidata":"https://www.wikidata.org/wiki/Q557945","display_name":"Confusion","level":2,"score":0.4763769805431366},{"id":"https://openalex.org/C146778888","wikidata":"https://www.wikidata.org/wiki/Q836862","display_name":"Installation","level":2,"score":0.45420002937316895},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4536033868789673},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.4260508418083191},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3240204453468323},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1423361599445343},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09076538681983948},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C11171543","wikidata":"https://www.wikidata.org/wiki/Q41630","display_name":"Psychoanalysis","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2022.893933","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.893933","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36304319","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36304319","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:ca02dad871fc4ee993941b8dfda2fee5","is_oa":true,"landing_page_url":"https://doaj.org/article/ca02dad871fc4ee993941b8dfda2fee5","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 2 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9580898","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9580898","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2022.893933","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.893933","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321945","display_name":"Ministry of Health, Labour and Welfare","ror":"https://ror.org/03mwa7s65"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1564554007","https://openalex.org/W1988925586","https://openalex.org/W2031611770","https://openalex.org/W2091922579","https://openalex.org/W2108718991","https://openalex.org/W2110417468","https://openalex.org/W2154026962","https://openalex.org/W2401404581","https://openalex.org/W2432815617","https://openalex.org/W2592367925","https://openalex.org/W2678211758","https://openalex.org/W2751013971","https://openalex.org/W2807194798","https://openalex.org/W2917207851","https://openalex.org/W2951912016","https://openalex.org/W2956439456","https://openalex.org/W2963276645","https://openalex.org/W2999369378","https://openalex.org/W3019168548","https://openalex.org/W3089811728","https://openalex.org/W3109937704","https://openalex.org/W3122109253","https://openalex.org/W3201353213","https://openalex.org/W3213732104","https://openalex.org/W4210644165"],"related_works":["https://openalex.org/W2391680869","https://openalex.org/W2392746298","https://openalex.org/W2383135875","https://openalex.org/W2363523615","https://openalex.org/W3022638154","https://openalex.org/W4390398439","https://openalex.org/W638541915","https://openalex.org/W2372114190","https://openalex.org/W4250798789","https://openalex.org/W4253103845"],"abstract_inverted_index":{"Optimizing":[0],"and":[1,21,24,31,45,59,70,75,88,90,98,116],"automating":[2],"a":[3,13,18,39,65,79],"protocol":[4],"for":[5],"16S":[6,47],"microbiome":[7],"data":[8,48,66],"analysis":[9,49,63,125],"with":[10],"QIIME2":[11],"is":[12,99],"challenging":[14],"task.":[15],"It":[16,83],"involves":[17],"multi-step":[19],"process,":[20],"multiple":[22,130],"parameters":[23],"options":[25],"that":[26,42],"need":[27],"to":[28,128],"be":[29],"tested":[30],"determined.":[32],"In":[33],"this":[34],"article,":[35],"we":[36],"describe":[37],"Snaq,":[38],"snakemake":[40],"pipeline":[41,107],"helps":[43],"automate":[44],"optimize":[46],"using":[50],"QIIME2.":[51],"Snaq":[52],"offers":[53],"an":[54],"informative":[55],"file":[56],"naming":[57],"system":[58],"automatically":[60],"performs":[61],"the":[62,72,94,111,118,122],"of":[64,96,124],"set":[67],"by":[68,102,121],"downloading":[69],"installing":[71],"required":[73],"databases":[74],"classifiers,":[76],"all":[77],"through":[78,93],"single":[80],"command-line":[81],"instruction.":[82],"works":[84],"natively":[85],"on":[86,91],"Linux":[87],"Mac":[89],"Windows":[92],"use":[95],"containers,":[97],"potentially":[100],"extendable":[101],"adding":[103],"new":[104],"rules.":[105],"This":[106],"will":[108],"substantially":[109],"reduce":[110],"efforts":[112],"in":[113],"sending":[114],"commands":[115],"prevent":[117],"confusion":[119],"caused":[120],"accumulation":[123],"results":[126],"due":[127],"testing":[129],"parameters.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
