{"id":"https://openalex.org/W7204276648","doi":"https://doi.org/10.5281/zenodo.22117210","title":"SARS-CoV-2 genomic surveillance: input snapshot and derived tables for a reproducible analysis pipeline","display_name":"SARS-CoV-2 genomic surveillance: input snapshot and derived tables for a reproducible analysis pipeline","publication_year":2026,"publication_date":"2026-08-14","ids":{"openalex":"https://openalex.org/W7204276648","doi":"https://doi.org/10.5281/zenodo.22117210"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22117210","doi":"https://doi.org/10.5281/zenodo.22117210","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22117210","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"volume":null,"type":"dataset","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22117210","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5148252037","display_name":"Soroush Sehat","orcid":"https://orcid.org/0009-0002-6272-9027","observed_orcids":["https://orcid.org/0009-0002-6272-9027"]},"institutions":[{"id":"https://openalex.org/I4210104933","display_name":"Biruni University","ror":"https://ror.org/01nkhmn89","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210104933"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Sehat, Soroush","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Biruni University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0009-0002-6272-9027","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Biruni University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4210104933"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5148252037"],"corresponding_institution_ids":["https://openalex.org/I4210104933"],"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/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9833999872207642,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9833999872207642,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.007600000128149986,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.0017000000225380063,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/sars-cov-2","display_name":"SARS-CoV-2","score":0.9990000128746033},{"id":"https://openalex.org/keywords/genomic-surveillance","display_name":"genomic surveillance","score":0.8420000076293945},{"id":"https://openalex.org/keywords/covid-19","display_name":"COVID-19 pandemic","score":0.75},{"id":"https://openalex.org/keywords/nextstrain","display_name":"Nextstrain","score":0.6340000033378601},{"id":"https://openalex.org/keywords/pango-lineages","display_name":"Pango lineages","score":0.8600000143051147},{"id":"https://openalex.org/keywords/spike-protein-mutations","display_name":"spike protein mutations","score":0.5929999947547913},{"id":"https://openalex.org/keywords/variant-frequency","display_name":"variant frequency","score":0.7429999709129333},{"id":"https://openalex.org/keywords/phylogeny","display_name":"phylogeny","score":0.5759999752044678},{"id":"https://openalex.org/keywords/dn-ds","display_name":"dN/dS","score":0.8510000109672546},{"id":"https://openalex.org/keywords/growth-advantage","display_name":"growth advantage","score":0.8479999899864197},{"id":"https://openalex.org/keywords/reproducible-analysis-pipeline","display_name":"reproducible analysis pipeline","score":0.6179999709129333}],"concepts":[{"id":"https://openalex.org/C162372511","wikidata":"https://www.wikidata.org/wiki/Q218341","display_name":"Checksum","level":2,"score":0.8113999962806702},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.7813000082969666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7591999769210815},{"id":"https://openalex.org/C43364308","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Byte","level":2,"score":0.6761000156402588},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5238999724388123},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.43959999084472656},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.37610000371932983},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35580000281333923},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.33959999680519104},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.32679998874664307},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.3240000009536743},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.30869999527931213},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.28459998965263367},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.28200000524520874},{"id":"https://openalex.org/C3115412","wikidata":"https://www.wikidata.org/wiki/Q1194708","display_name":"Bitmap","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2720000147819519},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.2651999890804291},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.25949999690055847},{"id":"https://openalex.org/C109751979","wikidata":"https://www.wikidata.org/wiki/Q998767","display_name":"Failover","level":2,"score":0.25040000677108765}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.22117210","doi":"https://doi.org/10.5281/zenodo.22117210","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22117210","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.22117211","doi":"https://doi.org/10.5281/zenodo.22117211","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22117211","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22117210","doi":"https://doi.org/10.5281/zenodo.22117210","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22117210","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"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/W6893357034","https://openalex.org/W6931087260","https://openalex.org/W7204524635","https://openalex.org/W6948235980","https://openalex.org/W7084573970","https://openalex.org/W6966743826","https://openalex.org/W3121673411","https://openalex.org/W6939348634","https://openalex.org/W7084622344","https://openalex.org/W4210415738"],"abstract_inverted_index":{"The":[0,25,227],"exact":[1],"input":[2,96,114],"snapshot":[3,57],"and":[4,41,48,109,153,159,168,175,190,200,234,248,274,283,294],"derived":[5,143],"output":[6],"tables":[7,144],"for":[8,112,269],"the":[9,28,61,69,78,95,101,119,137,142,218,222,231,237,251,254,266,270,275,292,299],"covid-genomics":[10],"analysis":[11],"pipeline,":[12],"deposited":[13,242],"so":[14,54],"that":[15,37,74],"its":[16,160],"figures":[17],"can":[18,64],"be":[19,304,310],"reproduced.":[20],"Why":[21],"this":[22,88,128],"deposit":[23],"exists.":[24],"pipeline":[26,102,120,232,300],"reads":[27],"Nextstrain":[29,202,252],"open":[30,258],"(GenBank/INSDC-derived)":[31],"100k":[32],"build":[33,79,255],"from":[34,217],"a":[35,56,125,176,281],"URL":[36],"carries":[38],"no":[39,42],"date":[40],"version.":[43],"It":[44,286],"is":[45,86,130,256,280,297,301],"refreshed":[46],"regularly":[47],"previous":[49],"contents":[50],"are":[51,135,211,215],"not":[52,236],"retrievable,":[53],"without":[55],"nobody":[58],"\u2014":[59,63,94,105,141,173],"including":[60],"author":[62],"reproduce":[65],"any":[66],"figure":[67],"in":[68,73,243,265,291],"repository.":[70],"Every":[71],"number":[72],"repository":[75,268],"corresponds":[76],"to":[77,99,146,303],"downloaded":[80],"on":[81],"11":[82],"August":[83],"2026,":[84],"which":[85],"what":[87,100],"record":[89,129],"contains.":[90],"Contents.":[91],"metadata.tsv.xz,":[92],"sequences.fasta.xz":[93],"snapshot,":[97],"byte-identical":[98],"downloaded.":[103],"manifest.json":[104],"SHA-256,":[106],"byte":[107],"size":[108],"fetch":[110],"time":[111],"each":[113,179],"file,":[115],"as":[116,312],"recorded":[117],"by":[118,221,245,250],"at":[121],"download":[122],"time.":[123],"Verifying":[124],"file":[126],"against":[127],"how":[131,298],"you":[132,134],"confirm":[133],"holding":[136],"same":[138],"bytes.":[139],"processed-tables.tar.gz":[140],"written":[145],"data/processed/:":[147],"quality-filter":[148],"cascade,":[149],"cleaned":[150],"metadata,":[151],"variant":[152],"mutation":[154],"frequency":[155],"series,":[156],"signature-mutation":[157],"recovery":[158],"threshold":[161],"sweep,":[162],"spike":[163],"annotation,":[164],"phylogenies,":[165],"growth-advantage":[166],"fits":[167],"dN/dS":[169],"estimates.":[170],"SHA256SUMS,":[171],"README.md":[172],"checksums":[174],"description":[177],"of":[178],"file.":[180],"Dataset.":[181],"62,159":[182],"quality-filtered":[183],"human":[184],"SARS-CoV-2":[185],"genomes":[186],"collected":[187],"between":[188],"2019-12-23":[189],"2026-07-25,":[191],"spanning":[192],"80":[193],"months,":[194],"129":[195],"countries,":[196],"2,969":[197],"Pango":[198],"lineages":[199],"59":[201],"clades.":[203],"Not":[204],"included.":[205],"Intermediate":[206],"alignment":[207],"products":[208],"(2.7":[209],"GB)":[210],"omitted":[212],"because":[213],"they":[214],"regenerated":[216],"inputs":[219],"above":[220],"pipeline's":[223],"own":[224],"steps.":[225],"Licensing.":[226],"MIT":[228],"licence":[229],"covers":[230],"code":[233],"figures,":[235],"genome":[238],"sequences.":[239],"Those":[240],"were":[241],"GenBank":[244],"laboratories":[246],"worldwide":[247],"curated":[249],"project;":[253],"INSDC-derived":[257],"data,":[259],"redistributable":[260],"with":[261],"attribution.":[262],"See":[263],"NOTICE.md":[264],"software":[267],"full":[271],"scope":[272],"statement":[273],"known-limitations":[276],"list.":[277],"Scope.":[278],"This":[279],"learning":[282],"portfolio":[284],"project.":[285],"reproduces":[287],"findings":[288],"already":[289],"established":[290],"literature,":[293],"reproducing":[295],"them":[296],"shown":[302],"correct.":[305],"No":[306],"result":[307],"here":[308],"should":[309],"cited":[311],"original":[313],"research.":[314]},"counts_by_year":[],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2026-08-27T00:00:00"}
