{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T17:56:41Z","timestamp":1788544601283,"version":"build-2803163510"},"reference-count":44,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T00:00:00Z","timestamp":1781827200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T00:00:00Z","timestamp":1781827200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["101059492"],"award-info":[{"award-number":["101059492"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Natural history collections are unparalleled archives of global biodiversity, yet most specimens remain molecularly uncharacterised due to the technical challenges of historical DNA (hDNA), including degradation, low endogenous content and contamination. Genome skimming offers a scalable alternative to PCR\u2010based barcoding, but existing bioinformatic workflows are not optimised for the heterogeneous, metagenomic nature of museum\u2010derived data. Here we present BeeGees (Barcode Extraction and Evaluation from Genome Skims), a high\u2010performance computing (HPC) integrated, Snakemake\u2010based workflow designed for protein\u2010guided recovery and validation of mitochondrial and plastid barcode genes from degraded short\u2010read genome sequences. BeeGees integrates dual read pre\u2010processing, systematic per\u2010sample parameter sweeps, sequential consensus cleaning to remove contaminant sequences and rigorous structural and taxonomic validation against curated reference databases. We benchmarked BeeGees on 1518 museum specimen\u2010derived genome skims spanning eight phyla. The workflow completed in approximately 120\u2009h (&lt;\u20095\u2009min per sample) on HPC infrastructure. When excluding sequencing failures (&lt;\u20091\u2009M reads), validated COI barcodes were recovered for 73.2% of specimens (1050\/1435). Barcode recovery success was influenced by endogenous content, preservation quality and parameter choice rather than raw read count alone, highlighting the importance of systematic parameter optimisation. Sequential consensus cleaning eliminated ambiguous bases and reduced chimeric artefacts, proving essential for robust museomic analyses. BeeGees provides a reproducible, scalable framework for high\u2010throughput barcode recovery and biodiversity genomics and reference gap\u2010filling initiatives from natural history collections. The BeeGees pipeline is available at:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/bge-barcoding\/BeeGees\/\">https:\/\/github.com\/bge\u2010barcoding\/BeeGees\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70170","type":"journal-article","created":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T13:07:27Z","timestamp":1781874447000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["BeeGees: A High\u2010Throughput Protein\u2010Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5246-0725","authenticated-orcid":false,"given":"Daniel A. J.","family":"Parsons","sequence":"first","affiliation":[{"name":"Natural History Museum  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9254-7318","authenticated-orcid":false,"given":"Rutger A.","family":"Vos","sequence":"additional","affiliation":[{"name":"Naturalis Biodiversity Center  Leiden the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5497-4087","authenticated-orcid":false,"given":"Benjamin W.","family":"Price","sequence":"additional","affiliation":[{"name":"Natural History Museum  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,6,19]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2025.09.001"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041\u2010210X.14075"},{"key":"e_1_2_11_4_1","unstructured":"Bushnell B.2014.\u201cBBMap: A Fast Accurate Splice\u2010Aware Aligner. 9th Annual Genomics of Energy & Environment Meeting Walnut Creek CA.\u201dhttps:\/\/bbmap.org."},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11475"},{"key":"e_1_2_11_6_1","volume-title":"BLAST Command Line Applications User Manual","author":"Camacho C.","year":"2024"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0905845106"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.10420"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12863\u2010022\u201001067\u20105"},{"key":"e_1_2_11_11_1","unstructured":"European Commission.2021.\u201cBig Data Analysis of Natural History Collections Shines a Light on Species Distribution.\u201dCORDIS | Accessed 2.23.26.https:\/\/cordis.europa.eu\/article\/id\/422197\u2010big\u2010data\u2010analysis\u2010of\u2010natural\u2010history\u2010collections\u2010shines\u2010a\u2010light\u2010on\u2010species\u2010distribution."},{"key":"e_1_2_11_12_1","unstructured":"Hall A. P.Cuber andB.Price.2023.\u201cLow\u2010Cost Museum DNA Extraction Using Magnetic Beads\u201d."},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2002.2218"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0068535"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12208"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13104\u2010016\u20102147\u20107"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esab012"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts480"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.3897\/rio.12.e187550"},{"key":"e_1_2_11_20_1","volume-title":"TrimGalore (Version 0.6.11)","author":"Krueger F.","year":"2024"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2013.00237"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2023.1260486"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010025\u201088443\u20100"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12380"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041\u2010210X.13945"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esad041"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.08456"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1002\/ppp3.10607"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13584"},{"key":"e_1_2_11_31_1","unstructured":"Price B.2025.\u201cMuseum Specimen Sampling SOP.\u201dhttps:\/\/doi.org\/10.48546\/WORKFLOWHUB.SOP.24.1."},{"key":"e_1_2_11_32_1","unstructured":"Price B. O.Powell A.Paul C.Gustave andJ.Beasley.2025.\u201cHistorical DNA Library Preparation (Spotlight).\u201dhttps:\/\/doi.org\/10.48546\/WORKFLOWHUB.SOP.22.1."},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12474"},{"key":"e_1_2_11_34_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.70043"},{"key":"e_1_2_11_35_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.11254"},{"key":"e_1_2_11_36_1","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2024"},{"key":"e_1_2_11_37_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066213"},{"key":"e_1_2_11_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.14121"},{"key":"e_1_2_11_39_1","volume-title":"MitoComp","author":"SamLMG","year":"2025"},{"key":"e_1_2_11_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mex.2019.06.001"},{"key":"e_1_2_11_41_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u20106\u201031"},{"key":"e_1_2_11_42_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7543"},{"key":"e_1_2_11_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt403"},{"key":"e_1_2_11_44_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.14036"},{"key":"e_1_2_11_45_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.70111"}],"container-title":["Molecular Ecology Resources"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.70170","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1755-0998.70170","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.70170","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T04:26:36Z","timestamp":1785299196000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.70170"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,19]]},"references-count":44,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,7]]}},"alternative-id":["10.1111\/1755-0998.70170"],"URL":"https:\/\/doi.org\/10.1111\/1755-0998.70170","archive":["Portico"],"relation":{},"ISSN":["1755-098X","1755-0998"],"issn-type":[{"value":"1755-098X","type":"print"},{"value":"1755-0998","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,19]]},"assertion":[{"value":"2026-03-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-04","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-19","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70170"}}