{"id":98870,"date":"2025-10-23T08:59:09","date_gmt":"2025-10-23T08:59:09","guid":{"rendered":"https:\/\/www.newsbeep.com\/ie\/98870\/"},"modified":"2025-10-23T08:59:09","modified_gmt":"2025-10-23T08:59:09","slug":"pararef-a-decontaminated-reference-database-for-parasite-detection-in-ancient-and-modern-metagenomic-datasets-genome-biology","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/ie\/98870\/","title":{"rendered":"ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets | Genome Biology"},"content":{"rendered":"

Blake DP, Betson M. One health: parasites and beyond. Parasitology. 2017;144:1\u20136.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Coulter JBS. Global importance of parasitic disease. Curr Paediatr. 2002;12:523\u201333.<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

World malaria report 2022. Geneva: World Health Organization; 2022. Licence: CC BY-NC-SA 3.0 IGO.<\/p>\n

Cox FEG. History of human parasitic diseases. Infect Dis Clin North Am. 2004;18:171\u201388.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bouchet F, Baffier D, Girard M, Morel P, Paicheler JC, David F. Palaeoparasitology in a Pleistocene context: initial observations in the Grande Grotte at Arcy-sur-Cure (Yonne), France. 1996.<\/p>\n

Kj\u00e6r KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, et al. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature. 2022;612:283\u201391.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Mitchell PD. Parasites in Past Civilizations and their Impact upon Health. Cambridge New York: Cambridge University Press; 2023.<\/p>\n

Mitchell PD. Ancient parasite analysis: exploring infectious diseases in past societies. J Archaeol Sci. 2024;170:106067.<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tams KW, Jensen S\u00f8e M, Merkyte I, Valeur Seersholm F, Henriksen PS, Klingenberg S, et al. Parasitic infections and resource economy of Danish iron age settlement through ancient DNA sequencing. PLoS ONE. 2018;13:e0197399.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Weiss JB. DNA probes and PCR for diagnosis of parasitic infections. Clin Microbiol Rev. 1995;8:113\u201330.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Singh B. Molecular methods for diagnosis and epidemiological studies of parasitic infections. Int J Parasitol. 1997;27:1135\u201345.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Valkiunas G, Iezhova TA, Krizanauskiene A, Palinauskas V, Sehgal RNM, Bensch S. A comparative analysis of microscopy and PCR-based detection methods for blood parasites. J Parasitol. 2008;94:1395\u2013401.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

S\u00f8e MJ, Nejsum P, Seersholm FV, Fredensborg BL, Habraken R, Haase K, et al. Ancient DNA from latrines in Northern Europe and the Middle East (500 BC\u20131700 AD) reveals past parasites and diet. PLoS ONE. 2018;13:e0195481.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019;20:341\u201355.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Franssen FFJ, Janse I, Janssen D, Caccio SM, Vatta P, van der Giessen JWB, et al. Mining public metagenomes for environmental surveillance of parasites: a proof of principle. Front Microbiol. 2021;12:622356.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. Front Bioinform. 2024;4:1278228.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Longo MS, O\u2019Neill MJ, O\u2019Neill RJ. Abundant human DNA contamination identified in non-primate genome databases. PLoS ONE. 2011;6:e16410.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

O\u2019Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733\u201345.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Astashyn A, Tvedte ES, Sweeney D, et al. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol. 2024;25:60.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Borner J, Burmester T. Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies. BMC Genomics. 2017;18:100.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Edwards RJ, Chen SH, Halliday B, Bragg JG. Small but mitey: a gapless telomere-to-telomere assembly of an unidentified mite with a streamlined genome. Genome Biol Evol. 2025;17(2):evaf023.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fierst JL, Murdock DA. Decontaminating eukaryotic genome assemblies with machine learning. BMC Bioinformatics. 2017;18:533.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Steinegger M, Salzberg SL. Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. Genome Biol. 2020;21:115.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021;22:178.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dirksen P, Assi\u00e9 A, Zimmermann J, Zhang F, Tietje AM, Marsh SA, et al. CeMbio – the caenorhabditis elegans microbiome resource. G3 Genes|Genomes|Genetics. 2020;10(9):3025\u201339.<\/p>\n

Ogier J-C, Pag\u00e8s S, Frayssinet M, Gaudriault S. Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome. Microbiome. 2020;8:25.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Grady EN, MacDonald J, Liu L, Richman A, Yuan Z-C. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact. 2016;15:203.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kulakov L, McAlister M, Ogden K, Larkin M, O\u2019Hanlon J. Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microbiol. 2002;68:1548\u201355.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007;315:207\u201312.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sabin S, Yeh H-Y, Pluskowski A, Clamer C, Mitchell PD, Bos KI. Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philos Trans R Soc Lond B Biol Sci. 2020;375:20190576.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, et al. Coproid predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ. 2020;8:e9001.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hagan RW, Hofman CA, H\u00fcbner A, Reinhard K, Schnorr S, Lewis CM Jr, et al. Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. Am J Phys Anthropol. 2020;171:275\u201384.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, et al. Hallstatt miners consumed blue cheese and beer during the iron age and retained a non-westernized gut microbiome until the baroque period. Curr Biol. 2021;31:5149-62.e6.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr SL, Hofman CA, et al. The gut microbiome buffers dietary adaptation in bronze age domesticated dogs. iScience. 2021;24:102816.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rifkin RF, Vikram S, Ramond J-B, Rey-Iglesia A, Brand TB, Porraz G, et al. Multi-proxy analyses of a mid-15th century middle iron age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the \u201cancestral\u201dsub-Saharan African intestinal microbiome. Microbiome. 2020;8:1\u201323.<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wibowo MC, Yang Z, Borry M, H\u00fcbner A, Huang KD, Tierney BT, et al. Reconstruction of ancient microbial genomes from the human gut. Nature. 2021;594:234\u20139.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Witt KE, Yarlagadda K, Allen JM, Bader AC, Simon ML, Kuehn SR, et al. Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet. Sci Rep. 2021;11:3113.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, et al. The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations. Cell Host Microbe. 2019;26:666-79.e7.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, et al. The 5300-year-old Helicobacter pylori genome of the Iceman. Science. 2016;351:162\u20135.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sarhan MS, Wurst C, Tzankov A, Bircher AJ, Wittig H, Briellmann T, et al. A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland. BMC Biol. 2023;21:9.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, et al. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell. 2023;186:3111-24.e13.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019;176:649-62.e20.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, et al. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries. Nat Microbiol. 2018;3:898\u2013908.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pochon Z, Bergfeldt N, K\u0131rd\u00f6k E, Vicente M, Naidoo T, van der Valk T, et al. Ameta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biol. 2023;24:242.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sikora M, Canteri E, Fernandez-Guerra A, Oskolkov N, \u00c5gren R, Hansson L, et al. The spatiotemporal distribution of human pathogens in ancient Eurasia. Nature. 2025;643:1011\u20139.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cook GC. Enterobius vermicularis infection. Gut. 1994;35:1159\u201362.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Traub RJ. Ancylostoma ceylanicum, a re-emerging but neglected parasitic zoonosis. Int J Parasitol. 2013;43:1009\u201315.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Greigert V, Abou-Bacar A, Brunet J, Nourrisson C, Pfaff AW, Benarbia L, et al. Human intestinal parasites in Mahajanga, Madagascar: the kingdom of the protozoa. PLoS One. 2018;13:e0204576.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Helwigh AB, Christensen CM, Roepstorff A, Nansen P. Concurrent Ascaris suum and Oesophagostomum dentatum infections in pigs. Vet Parasitol. 1999;82:221\u201334.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Santos SS, de Ara\u00fajo RV, Giarolla J, Seoud OE, Ferreira EI. Searching for drugs for Chagas disease, leishmaniasis and schistosomiasis: a review. Int J Antimicrob Agents. 2020;55:105906.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, et al. Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS Glob Public Health. 2023;3:e0001675.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yang Z, Kasprzyk-Hordern B, Frost CG, Estrela P, Thomas KV. Community sewage sensors for monitoring public health. Environ Sci Technol. 2015;49:5845\u20136.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Whibley A, Kelley JL, Narum SR. The changing face of genome assemblies: guidance on achieving high-quality reference genomes. Mol Ecol Resour. 2021;21:641\u201352.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, et al. Genomics in the long-read sequencing era. Trends Genet. 2023;39:649\u201371.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

de la Torre P, Merchant MT, Willms K, Laclette JP. Host cells in the spiral canal of Taenia solium (cestoda) cysticerci. J Parasitol. 1998;84:167\u201371.<\/p>\n

PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dickson JH, Oeggl K, Holden TG, Handley LL, O\u2019Connell TC, Preston T. The omnivorous Tyrolean Iceman: colon contents (meat, cereals, pollen, moss and whipworm) and stable isotope analyses. Philos Trans R Soc Lond B Biol Sci. 2000;355:1843\u20139.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Oskolkov N, Sandionigi A, G\u00f6therstr\u00f6m A, et al. Unraveling the ancient fungal DNA from the Iceman gut. BMC Genomics. 2024;25:1225.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Schwartze VU, Hoffmann K, Nyilasi I, Papp T, V\u00e1gv\u00f6lgyi C, de Hoog S, et al. Lichtheimia species exhibit differences in virulence potential. PLoS One. 2012;7:e40908.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Popruk S, Adao DEV, Rivera WL. Epidemiology and subtype distribution of Blastocystis in humans: a review. Infect Genet Evol. 2021;95:105085.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

AQ Kirstahler P, Aarestrup FM, Pamp SJ. Detection of parasites in microbiomes using metagenomics. bioRxiv. 2022:2022.03.27.485979.<\/p>\n

Hotez PJ, Fenwick A. Schistosomiasis in Africa: an emerging tragedy in our new global health decade. PLoS Negl Trop Dis. 2009;3:e485.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Breitwieser FP, Baker DN, Salzberg SL. Krakenuniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biol. 2018;19:198.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, et al. imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ. 2018;6:e5882.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nagar A, Hahsler M. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC Bioinformatics. 2013;14(Suppl 11):S2.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Ba\u017cant W, et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022;50:D898-911.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

O\u2019Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, et al. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI datasets. Sci Data. 2024;11:732.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Sherry ST, Yankie L, et al. GenBank 2023 update. Nucleic Acids Res. 2023;51:D141\u20134.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Quinlan AR, Hall IM. BEDtools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u20132.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Renaud G, Hangh\u00f8j K, Willerslev E, Orlando L. gargammel: a sequence simulator for ancient DNA. Bioinformatics. 2017;33:577\u20139.<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ferragina P, Manzini G. Opportunistic data structures with applications. Proceedings 41st Annual Symposium on Foundations of Computer Science, Redondo Beach, CA, USA. 2000;390\u2013398. https:\/\/doi.org\/10.1109\/SFCS.2000.892127<\/a>.<\/p>\n

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10:giab008.<\/p>\n

R Core Team. R: A language and environment for statistical computing. R foundation for statistical computing.\u00a0Vienna, Austria: 2024.<\/p>\n

Fellows Yates JA, Andrades Valtue\u00f1a A, V\u00e5gene \u00c5J, Cribdon B, Velsko IM, Borry M, et al. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data. 2021;8:31.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtue\u00f1a A, Fagern\u00e4s Z, Clayton S, et al. Reproducible, portable, and efficient ancient genome reconstruction with nf-core\/eager. PeerJ. 2021;9:e10947.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Michelsen C, Pedersen MW, Fernandez-Guerra A, Zhao L, Petersen TC, Korneliussen TS. MetaDMG \u2013 a fast and accurate ancient DNA damage toolkit for metagenomic data. bioRxiv. 2022; Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2022.12.06.519264v1<\/a>.<\/p>\n

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Niemann J, Huang Y, Lanigan LT, Willingham-Grijalba AL, Dunn RR, Sikora M, Schroeder H. ParaRef: decontaminated parasite reference database. Github. 2025. https:\/\/doi.org\/10.5281\/zenodo.17193190<\/a>.<\/p>\n

Niemann J, Huang Y, Lanigan LT, Willingham-Grijalba AL, Dunn RR, Sikora M, Schroeder H. ParaRef. Zenodo. 2025. https:\/\/doi.org\/10.5281\/zenodo.13744644<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"Blake DP, Betson M. One health: parasites and beyond. Parasitology. 2017;144:1\u20136. PubMed\u00a0 Google Scholar\u00a0 Coulter JBS. Global importance…\n","protected":false},"author":2,"featured_media":98871,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[5209,4790,6835,5207,61,60,6834,6833,82],"class_list":{"0":"post-98870","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-animal-genetics-and-genomics","9":"tag-bioinformatics","10":"tag-evolutionary-biology","11":"tag-human-genetics","12":"tag-ie","13":"tag-ireland","14":"tag-microbial-genetics-and-genomics","15":"tag-plant-genetics-and-genomics","16":"tag-science"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/posts\/98870","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/comments?post=98870"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/posts\/98870\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/media\/98871"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/media?parent=98870"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/categories?post=98870"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/ie\/wp-json\/wp\/v2\/tags?post=98870"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}