{"id":"https://openalex.org/W4389453417","doi":"https://doi.org/10.3389/fbinf.2023.1260486","title":"Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA","display_name":"Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA","publication_year":2023,"publication_date":"2023-12-07","ids":{"openalex":"https://openalex.org/W4389453417","doi":"https://doi.org/10.3389/fbinf.2023.1260486","pmid":"https://pubmed.ncbi.nlm.nih.gov/38131007"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1260486","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1260486","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1260486/pdf?isPublishedV2=False","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://www.frontiersin.org/articles/10.3389/fbinf.2023.1260486/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050615876","display_name":"Annette Lien","orcid":"https://orcid.org/0009-0006-0578-9225"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Annette Lien","raw_affiliation_strings":["Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003618550","display_name":"Leonardo Pestana Legori","orcid":"https://orcid.org/0000-0002-4169-2336"},"institutions":[{"id":"https://openalex.org/I132735039","display_name":"University of Debrecen","ror":"https://ror.org/02xf66n48","country_code":"HU","type":"education","lineage":["https://openalex.org/I132735039"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Leonardo Pestana Legori","raw_affiliation_strings":["University of Debrecen, Debrecen, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Debrecen, Debrecen, Hungary","institution_ids":["https://openalex.org/I132735039"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077482080","display_name":"Louis Kraft","orcid":"https://orcid.org/0000-0002-6465-4973"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Louis Kraft","raw_affiliation_strings":["Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064396074","display_name":"Peter Wad Sackett","orcid":"https://orcid.org/0000-0003-3628-2807"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Peter Wad Sackett","raw_affiliation_strings":["Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023722162","display_name":"Gabriel Renaud","orcid":"https://orcid.org/0000-0002-0630-027X"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Gabriel Renaud","raw_affiliation_strings":["Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5023722162"],"corresponding_institution_ids":["https://openalex.org/I96673099"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":1.4141,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.82107305,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"3","issue":null,"first_page":"1260486","last_page":"1260486"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10751","display_name":"Forensic and Genetic Research","score":0.9994000196456909,"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"}},{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9951000213623047,"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/adapter","display_name":"Adapter (computing)","score":0.847734272480011},{"id":"https://openalex.org/keywords/trimming","display_name":"Trimming","score":0.6270684599876404},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6125923991203308},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5552463531494141},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.554881751537323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4894651174545288},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47141191363334656},{"id":"https://openalex.org/keywords/ancient-dna","display_name":"Ancient DNA","score":0.44958850741386414},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.38420814275741577},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34656763076782227},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32368361949920654},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26929351687431335},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24362120032310486},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2247200310230255},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.1134052574634552}],"concepts":[{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.847734272480011},{"id":"https://openalex.org/C56951928","wikidata":"https://www.wikidata.org/wiki/Q3539213","display_name":"Trimming","level":2,"score":0.6270684599876404},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6125923991203308},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5552463531494141},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.554881751537323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4894651174545288},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47141191363334656},{"id":"https://openalex.org/C189338579","wikidata":"https://www.wikidata.org/wiki/Q290447","display_name":"Ancient DNA","level":3,"score":0.44958850741386414},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.38420814275741577},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34656763076782227},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32368361949920654},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26929351687431335},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24362120032310486},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2247200310230255},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.1134052574634552},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2023.1260486","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1260486","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1260486/pdf?isPublishedV2=False","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:38131007","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38131007","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:pubmedcentral.nih.gov:10733496","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10733496","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10733496/pdf/fbinf-03-1260486.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d2501efae46b4b3187554853853454cc","is_oa":true,"landing_page_url":"https://doaj.org/article/d2501efae46b4b3187554853853454cc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1260486","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1260486","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1260486/pdf?isPublishedV2=False","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":[{"id":"https://openalex.org/G1146216518","display_name":null,"funder_award_id":"NNF20OC0062491","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389453417.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W2050967443","https://openalex.org/W2103441770","https://openalex.org/W2110417468","https://openalex.org/W2120048439","https://openalex.org/W2136068873","https://openalex.org/W2137591261","https://openalex.org/W2157539385","https://openalex.org/W2263582186","https://openalex.org/W2301949952","https://openalex.org/W2319185332","https://openalex.org/W2544029679","https://openalex.org/W2575981814","https://openalex.org/W2593742724","https://openalex.org/W2616754551","https://openalex.org/W2765281411","https://openalex.org/W2791904732","https://openalex.org/W2802139569","https://openalex.org/W2805217760","https://openalex.org/W2887731084","https://openalex.org/W2951214697","https://openalex.org/W2951912016","https://openalex.org/W2952870794","https://openalex.org/W3007203867","https://openalex.org/W3009339878","https://openalex.org/W3087682297","https://openalex.org/W3095965818","https://openalex.org/W3129075539","https://openalex.org/W3131055609","https://openalex.org/W3161461466","https://openalex.org/W4205547614","https://openalex.org/W4213456315","https://openalex.org/W4220999759","https://openalex.org/W4247053599","https://openalex.org/W4292313500","https://openalex.org/W4293092677","https://openalex.org/W4298395572","https://openalex.org/W4302288380","https://openalex.org/W4315631570","https://openalex.org/W4360827699","https://openalex.org/W4366140926"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W2086381437","https://openalex.org/W4391340216","https://openalex.org/W2119276480","https://openalex.org/W4389452249","https://openalex.org/W2905822234"],"abstract_inverted_index":{"Ancient":[0],"DNA":[1,22,53,118],"is":[2,36,147,213],"highly":[3],"degraded,":[4],"resulting":[5],"in":[6,112,129,149,189,200],"very":[7],"short":[8],"sequences.":[9],"Reads":[10],"generated":[11],"with":[12,46],"modern":[13],"high-throughput":[14],"sequencing":[15,33,66,104],"machines":[16],"are":[17,221],"generally":[18],"longer":[19],"than":[20],"ancient":[21,117],"molecules,":[23],"therefore":[24],"the":[25,32,101,138,143,160,186,193,238],"reads":[26,226],"often":[27],"contain":[28],"some":[29,173,179],"portion":[30],"of":[31,103,195,240],"adaptors.":[34],"It":[35],"crucial":[37],"to":[38,64,88,115,132,152,215,223],"remove":[39],"those":[40],"adaptors,":[41],"as":[42,176],"they":[43],"can":[44,61,233],"interfere":[45],"downstream":[47,98,218],"analysis.":[48],"Furthermore,":[49],"overlapping":[50],"portions":[51],"when":[52,204],"has":[54,86],"been":[55,75],"read":[56,70,81,121,140],"forward":[57],"and":[58,68,80,92,136],"backward":[59],"(paired-end)":[60],"be":[62,234],"merged":[63,157,225],"correct":[65,133,139],"errors":[67,135],"improve":[69],"quality.":[71],"Several":[72],"tools":[73,109,125,174,188],"have":[74,178],"developed":[76],"for":[77,156,164],"adapter":[78],"trimming":[79],"merging,":[82],"however,":[83],"no":[84],"one":[85],"attempted":[87],"evaluate":[89,93],"their":[90,94,113,130,150],"accuracy":[91],"potential":[95],"impact":[96],"on":[97,169,230],"analyses.":[99],"Through":[100],"simulation":[102],"data,":[105],"seven":[106],"commonly":[107],"used":[108],"were":[110],"analyzed":[111,124],"ability":[114,151],"reconstruct":[116],"sequences":[119],"through":[120],"merging.":[122],"The":[123],"exhibit":[126],"notable":[127],"differences":[128],"abilities":[131],"sequence":[134],"identify":[137],"overlap,":[141],"but":[142],"most":[144,161,190],"substantial":[145],"difference":[146,203],"observed":[148],"calculate":[153],"quality":[154,231],"scores":[155,232],"bases.":[158],"Selecting":[159],"appropriate":[162],"tool":[163,196],"a":[165,201],"given":[166],"project":[167],"depends":[168],"several":[170],"factors,":[171],"although":[172],"such":[175],"fastp":[177],"shortcomings,":[180],"whereas":[181],"others":[182],"like":[183],"leeHom":[184],"outperform":[185],"other":[187],"aspects.":[191],"While":[192],"choice":[194,239],"did":[197],"not":[198],"result":[199],"measurable":[202],"analyzing":[205],"population":[206],"genetics":[207],"using":[208],"principal":[209],"component":[210],"analysis,":[211],"it":[212],"important":[214],"note":[216],"that":[217,220,228],"analyses":[219],"sensitive":[222],"wrongly":[224],"or":[227],"rely":[229],"significantly":[235],"impacted":[236],"by":[237],"tool.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
