{"id":"https://openalex.org/W2804892997","doi":"https://doi.org/10.1101/326363","title":"Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments","display_name":"Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments","publication_year":2018,"publication_date":"2018-05-18","ids":{"openalex":"https://openalex.org/W2804892997","doi":"https://doi.org/10.1101/326363","mag":"2804892997"},"language":"en","primary_location":{"id":"doi:10.1101/326363","doi":"https://doi.org/10.1101/326363","is_oa":true,"landing_page_url":"https://doi.org/10.1101/326363","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/29/326363.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/29/326363.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002280838","display_name":"Erik Clarke","orcid":"https://orcid.org/0000-0002-2031-8791","observed_orcids":["https://orcid.org/0000-0002-2031-8791"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik L. Clarke","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania","Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904"],"raw_orcid":"https://orcid.org/0000-0002-2031-8791","affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032070246","display_name":"Louis J. Taylor","orcid":"https://orcid.org/0000-0002-6993-5838","observed_orcids":["https://orcid.org/0000-0002-6993-5838"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louis J. Taylor","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania","Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904"],"raw_orcid":"https://orcid.org/0000-0002-6993-5838","affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101571739","display_name":"Chunyu Zhao","orcid":"https://orcid.org/0000-0001-9589-2416","observed_orcids":["https://orcid.org/0000-0001-9589-2416"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunyu Zhao","raw_affiliation_strings":["Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065039823","display_name":"Andrew Jesse Connell","orcid":"https://orcid.org/0000-0002-9393-3074","observed_orcids":["https://orcid.org/0000-0002-9393-3074"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Connell","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania","Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904"],"raw_orcid":"https://orcid.org/0000-0002-9393-3074","affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101667988","display_name":"Jung\u2010Jin Lee","orcid":"https://orcid.org/0000-0003-1025-8980","observed_orcids":["https://orcid.org/0000-0003-1025-8980"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jung-Jin Lee","raw_affiliation_strings":["Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034438642","display_name":"Bryton Fett","orcid":"https://orcid.org/0000-0001-9017-7771","observed_orcids":["https://orcid.org/0000-0001-9017-7771"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryton Fett","raw_affiliation_strings":["Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016535188","display_name":"Frederic D. Bushman","orcid":"https://orcid.org/0000-0003-4740-4056","observed_orcids":["https://orcid.org/0000-0003-4740-4056"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frederic D. Bushman","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania","Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904"],"raw_orcid":"https://orcid.org/0000-0003-4740-4056","affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 904","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066967353","display_name":"Kyle L. Bittinger","orcid":"https://orcid.org/0000-0003-3472-5934","observed_orcids":["https://orcid.org/0000-0003-3472-5934"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kyle Bittinger","raw_affiliation_strings":["Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104","institution_ids":["https://openalex.org/I1335321130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066967353"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":26,"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":0.9965999722480774,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T11986","display_name":"Scientific Computing and Data Management","score":0.0008999999845400453,"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"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.0003000000142492354,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/sunbeam","display_name":"Sunbeam","score":0.8059999942779541},{"id":"https://openalex.org/keywords/metagenomics-pipeline","display_name":"metagenomics pipeline","score":0.7799999713897705},{"id":"https://openalex.org/keywords/microbial-community-analysis","display_name":"microbial community analysis","score":0.6970000267028809},{"id":"https://openalex.org/keywords/adapter-trimming","display_name":"adapter trimming","score":0.7940000295639038},{"id":"https://openalex.org/keywords/metagenomic-classification","display_name":"metagenomic classification","score":0.8209999799728394},{"id":"https://openalex.org/keywords/read-assembly","display_name":"read assembly","score":0.7170000076293945},{"id":"https://openalex.org/keywords/reproducible-analysis","display_name":"reproducible analysis","score":0.5529999732971191},{"id":"https://openalex.org/keywords/snakemake-workflow","display_name":"Snakemake workflow","score":0.753000020980835}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8818007707595825},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6901482939720154},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6517118811607361},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5474938154220581},{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.5231379270553589},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5189842581748962},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.49093344807624817},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4296560287475586},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.4172239601612091},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4123395085334778},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3584754467010498},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3361048400402069},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23867163062095642},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20749154686927795},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1938115358352661},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16368001699447632},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1101/326363","doi":"https://doi.org/10.1101/326363","is_oa":true,"landing_page_url":"https://doi.org/10.1101/326363","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/29/326363.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:zenodo.org:1287807","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/1287807","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"}],"best_oa_location":{"id":"doi:10.1101/326363","doi":"https://doi.org/10.1101/326363","is_oa":true,"landing_page_url":"https://doi.org/10.1101/326363","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/29/326363.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5393834668","display_name":"Training in Virology","funder_award_id":"T32AI007324","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8173708265","display_name":"Lung Transplant Microbiome and Chronic Allograft Dysfunction","funder_award_id":"R01HL113252","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G9000887542","display_name":"Penn Center for AIDS Research","funder_award_id":"P30AI045008","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332582","display_name":"Center for AIDS Research, University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2804892997.pdf","grobid_xml":"https://content.openalex.org/works/W2804892997.grobid-xml"},"referenced_works_count":100,"referenced_works":["https://openalex.org/W1497287772","https://openalex.org/W1499500424","https://openalex.org/W1550594300","https://openalex.org/W1703384511","https://openalex.org/W1911384112","https://openalex.org/W1958058086","https://openalex.org/W1970707135","https://openalex.org/W1973862547","https://openalex.org/W1974575979","https://openalex.org/W1989021204","https://openalex.org/W2000040814","https://openalex.org/W2009906332","https://openalex.org/W2020504063","https://openalex.org/W2021341670","https://openalex.org/W2023645032","https://openalex.org/W2031611770","https://openalex.org/W2036897871","https://openalex.org/W2040805829","https://openalex.org/W2045204781","https://openalex.org/W2046321131","https://openalex.org/W2055043387","https://openalex.org/W2071103029","https://openalex.org/W2071501400","https://openalex.org/W2074668828","https://openalex.org/W2077317706","https://openalex.org/W2079958213","https://openalex.org/W2095685450","https://openalex.org/W2096093282","https://openalex.org/W2096525273","https://openalex.org/W2101735289","https://openalex.org/W2103441770","https://openalex.org/W2103539617","https://openalex.org/W2103962160","https://openalex.org/W2108234281","https://openalex.org/W2110417468","https://openalex.org/W2111973517","https://openalex.org/W2112814753","https://openalex.org/W2112874908","https://openalex.org/W2116041602","https://openalex.org/W2117752525","https://openalex.org/W2120902911","https://openalex.org/W2124937554","https://openalex.org/W2130731460","https://openalex.org/W2131026689","https://openalex.org/W2131186249","https://openalex.org/W2131271579","https://openalex.org/W2131342905","https://openalex.org/W2137662380","https://openalex.org/W2139353300","https://openalex.org/W2143485490","https://openalex.org/W2143777796","https://openalex.org/W2143788241","https://openalex.org/W2145370398","https://openalex.org/W2146155123","https://openalex.org/W2151429702","https://openalex.org/W2154364831","https://openalex.org/W2154969437","https://openalex.org/W2155860422","https://openalex.org/W2159954944","https://openalex.org/W2162088497","https://openalex.org/W2167062509","https://openalex.org/W2167155938","https://openalex.org/W2169474803","https://openalex.org/W2170551349","https://openalex.org/W2171787842","https://openalex.org/W2226299262","https://openalex.org/W2255506873","https://openalex.org/W2293713895","https://openalex.org/W2303656007","https://openalex.org/W2310864030","https://openalex.org/W2337747100","https://openalex.org/W2462800864","https://openalex.org/W2509730012","https://openalex.org/W2513506562","https://openalex.org/W2529965014","https://openalex.org/W2558135510","https://openalex.org/W2579012589","https://openalex.org/W2589351926","https://openalex.org/W2592634345","https://openalex.org/W2599417231","https://openalex.org/W2611561371","https://openalex.org/W2611957242","https://openalex.org/W2747591836","https://openalex.org/W2754579667","https://openalex.org/W2797908553","https://openalex.org/W2802528759","https://openalex.org/W2803457956","https://openalex.org/W2806631703","https://openalex.org/W2884696611","https://openalex.org/W2887136521","https://openalex.org/W2891286508","https://openalex.org/W2891335288","https://openalex.org/W2897603717","https://openalex.org/W2899101060","https://openalex.org/W2952615074","https://openalex.org/W2977180444","https://openalex.org/W4230784961","https://openalex.org/W4234583126","https://openalex.org/W4254687493","https://openalex.org/W6608097372"],"related_works":["https://openalex.org/W4388479606","https://openalex.org/W7206360834","https://openalex.org/W4416535827","https://openalex.org/W3023627704","https://openalex.org/W4412492460","https://openalex.org/W4362736020","https://openalex.org/W3094445727","https://openalex.org/W4411695985","https://openalex.org/W2169230701","https://openalex.org/W7153012834"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Analysis":[2],"of":[3,24,109,116],"mixed":[4],"microbial":[5,20],"communities":[6],"using":[7,190],"metagenomic":[8,35,105,170],"sequencing":[9,171],"experiments":[10,172],"requires":[11],"multiple":[12],"preprocessing":[13],"and":[14,21,39,49,61,82,121,142,152,165,179,182,196],"analytical":[15,183],"steps":[16,27,57,135],"to":[17,41,77,97,129,137,160,166],"interpret":[18],"the":[19,78,110,138,191,203],"genetic":[22],"composition":[23],"samples.":[25],"Analytical":[26],"include":[28,113],"quality":[29],"control,":[30],"adapter":[31],"trimming,":[32],"host":[33,79],"decontamination,":[34],"classification,":[36],"read":[37],"assembly,":[38],"alignment":[40],"reference":[42],"genomes.":[43],"Results":[44],"We":[45,90],"present":[46],"a":[47,59,69,94,158],"modular":[48],"user-extensible":[50],"pipeline":[51,112,141],"called":[52],"Sunbeam":[53,111,156,185],"that":[54,126],"performs":[55],"these":[56],"in":[58,68,149,169,188],"consistent":[60],"reproducible":[62],"fashion.":[63],"It":[64],"can":[65,83],"be":[66],"installed":[67],"single":[70],"step,":[71],"does":[72],"not":[73],"require":[74],"administrative":[75],"access":[76],"computer":[80],"system,":[81],"work":[84],"with":[85],"most":[86],"cluster":[87],"computing":[88],"frameworks.":[89],"also":[91],"introduce":[92],"Komplexity,":[93],"software":[95,195],"tool":[96],"eliminate":[98],"potentially":[99],"problematic,":[100],"low-complexity":[101],"nucleotide":[102],"sequences":[103],"from":[104,118],"data.":[106],"Unique":[107],"components":[108],"direct":[114],"analysis":[115,134],"data":[117],"NCBI":[119],"SRA":[120],"an":[122],"easy-to-use":[123],"extension":[124,144],"framework":[125,145],"enables":[127],"users":[128],"add":[130],"custom":[131],"processing":[132],"or":[133],"directly":[136],"workflow.":[139],"The":[140],"its":[143],"are":[146],"well":[147],"documented,":[148],"routine":[150],"use,":[151],"regularly":[153],"updated.":[154],"Conclusions":[155],"provides":[157],"foundation":[159],"build":[161],"more":[162],"in-depth":[163],"analyses":[164],"enable":[167],"comparisons":[168],"by":[173],"removing":[174],"problematic":[175],"low":[176],"complexity":[177],"reads":[178],"standardizing":[180],"post-processing":[181],"steps.":[184],"is":[186,197],"written":[187],"Python":[189],"Snakemake":[192],"workflow":[193],"management":[194],"freely":[198],"available":[199],"at":[200],"github.com/sunbeam-labs/sunbeam":[201],"under":[202],"GPLv3.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2018-06-01T00:00:00"}