{"id":"https://openalex.org/W2902958465","doi":"https://doi.org/10.7287/peerj.preprints.27272v1","title":"Hundo: a Snakemake workflow for microbial community sequence data","display_name":"Hundo: a Snakemake workflow for microbial community sequence data","publication_year":2018,"publication_date":"2018-10-10","ids":{"openalex":"https://openalex.org/W2902958465","doi":"https://doi.org/10.7287/peerj.preprints.27272v1","mag":"2902958465"},"language":"en","primary_location":{"id":"doi:10.7287/peerj.preprints.27272v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27272v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7287/peerj.preprints.27272v1","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102838242","display_name":"Joseph Brown","orcid":"https://orcid.org/0000-0002-7678-6105"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph Brown","raw_affiliation_strings":["Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States"],"affiliations":[{"raw_affiliation_string":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023642910","display_name":"Nicole Zavoshy","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Zavoshy","raw_affiliation_strings":["Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States"],"affiliations":[{"raw_affiliation_string":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000856048","display_name":"Colin Brislawn","orcid":"https://orcid.org/0000-0002-9109-1950"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin J Brislawn","raw_affiliation_strings":["Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States"],"affiliations":[{"raw_affiliation_string":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055701440","display_name":"Lee Ann McCue","orcid":"https://orcid.org/0000-0003-4456-517X"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lee Ann McCue","raw_affiliation_strings":["Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States"],"affiliations":[{"raw_affiliation_string":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States","institution_ids":["https://openalex.org/I142606810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102838242"],"corresponding_institution_ids":["https://openalex.org/I142606810"],"apc_list":null,"apc_paid":null,"fwci":1.5627,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.83729078,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"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":0.9995999932289124,"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":0.9995999932289124,"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":0.994700014591217,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9872000217437744,"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/workflow","display_name":"Workflow","score":0.8038780689239502},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7147635817527771},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7055903077125549},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6996960639953613},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6618306636810303},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6163762807846069},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.6010082364082336},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5775591135025024},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.519226610660553},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.47570452094078064},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42094919085502625},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34268343448638916},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33068710565567017},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.223859041929245},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15945780277252197}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8038780689239502},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7147635817527771},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7055903077125549},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6996960639953613},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6618306636810303},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6163762807846069},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.6010082364082336},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5775591135025024},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.519226610660553},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.47570452094078064},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42094919085502625},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34268343448638916},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33068710565567017},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.223859041929245},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15945780277252197},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.7287/peerj.preprints.27272v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27272v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.7287/peerj.preprints.27272v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27272v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W4231704780","https://openalex.org/W1516095885","https://openalex.org/W2158573927","https://openalex.org/W2108921801","https://openalex.org/W1981336497"],"abstract_inverted_index":{"Hundo":[0],"is":[1,56,63],"a":[2,22],"software":[3,52],"package":[4,53],"that":[5,29],"performs":[6],"quality":[7],"control":[8],"and":[9,14,27,67,75],"annotation":[10,39,55],"of":[11,25,35,45],"ribosomal":[12],"RNA":[13],"internal":[15],"transcribed":[16],"spacer":[17],"sequence":[18,38],"reads.":[19],"It":[20],"provides":[21],"comprehensive":[23],"suite":[24],"tools":[26],"options":[28],"aim":[30],"to":[31,48],"reduce":[32],"the":[33,42,60,76,83],"effort":[34],"performing":[36,54],"robust":[37],"while":[40],"obtaining":[41],"maximum":[43],"amount":[44],"data":[46],"provenance":[47],"ensure":[49],"replicability.":[50],"The":[51],"implemented":[57,64],"in":[58,65],"Python,":[59],"analytical":[61],"workflow":[62],"Snakemake,":[66],"dependencies":[68],"are":[69,80],"installed":[70],"via":[71],"Bioconda.":[72],"Extensive":[73],"documentation":[74],"full":[77],"source":[78],"code":[79],"available":[81],"under":[82],"MIT":[84],"license":[85],"at:":[86],"https://github.com/pnnl/hundo":[87],".":[88]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
