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aMeta :
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Pochon, ZoéStockholm University,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
(author)
aMeta : an accurate and memory-efficient ancient metagenomic profiling workflow
- Article/chapterEnglish2023
Publisher, publication year, extent ...
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BioMed Central (BMC),2023
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printrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:su-224292
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https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-224292URI
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https://doi.org/10.1186/s13059-023-03083-9DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-516926URI
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https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-199457URI
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https://lup.lub.lu.se/record/ac4a000b-898b-4b7a-bece-a682a7c0dfc4URI
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https://urn.kb.se/resolve?urn=urn:nbn:se:nrm:diva-5333URI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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Funding Agencies|Lund University; Knut and Alice Wallen-berg Foundation, National Bioinformatics Infrastructure Sweden at SciLifeLab; Swedish Research Council [2018-05973, SNIC 2021/5-335, SNIC 2021/6-260, SNIC 2022/5-100, SNIC 2022/6-46, SNIC 2022/22-507, SNIC 2022/23-275]; Mersin University BAP [2019-3-AP3-3729]; Swedish Research Council (VR) [2019-00849]
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Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Bergfeldt, NoraStockholm University,Swedish Museum of Natural History,Stockholms universitet,Zoologiska institutionen,Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.(Swepub:su)nobe0210
(author)
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Kirdök, EmrahMersin Univ, Fac Sci, Dept Biotechnol, Mersin, Turkey.,Mersin University
(author)
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Vicente, MárioStockholm University,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.(Swepub:su)mavi0191
(author)
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Naidoo, ThijessenStockholm University,Uppsala universitet,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Science for Life Laboratory (SciLifeLab),Centre for Palaeogenetics, Sweden,Science for Life Laboratory, SciLifeLab,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.;Sci Life Lab, Ancient DNA Unit, Stockholm, Sweden.(Swepub:uu)thina233
(author)
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van der Valk, TomNaturhistoriska riksmuseet,Swedish Museum of Natural History,Enheten för bioinformatik och genetik(Swepub:nrm)tomvande
(author)
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Altınışık, N. EzgiHacettepe Univ, Dept Anthropol, Human G Lab, TR-06800 Beytepe, Ankara, Turkey.,Hacettepe University
(author)
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Krzewińska, Maja,1978-Stockholm University,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.(Swepub:su)mkrze
(author)
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Dalén, Love,1980-Stockholm University,Stockholms universitet,Zoologiska institutionen,Centre for Palaeogenetics, Sweden,Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.(Swepub:lu)lo8440da
(author)
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Götherström, Anders,1969-Stockholm University,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Ctr Palaeogenet, Sweden; Stockholm Univ, Sweden(Swepub:su)gother
(author)
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Mirabello, ClaudioLinköping University,Linköpings universitet,Bioinformatik,Tekniska fakulteten(Swepub:liu)clami66
(author)
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Unneberg, PerUppsala University,Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab,National Bioinformatics Infrastructure Sweden,Uppsala Univ, Sweden(Swepub:uu)perun990
(author)
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Oskolkov, NikolayLund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Bioinformatik,Forskargrupper vid Lunds universitet,LTH profilområde: Teknik för hälsa,LTH profilområden,Lunds Tekniska Högskola,Molecular Cell Biology,Department of Biology,Faculty of Science,Bioinformatics,Lund University Research Groups,LTH Profile Area: Engineering Health,LTH Profile areas,Faculty of Engineering, LTH(Swepub:lu)med-nao
(author)
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Stockholms universitetInstitutionen för arkeologi och antikens kultur
(creator_code:org_t)
Related titles
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In:Genome Biology: BioMed Central (BMC)241465-69061474-760X
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In:Genome Biology: BioMed Central (BMC)241474-7596
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- By the author/editor
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Pochon, Zoé
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Bergfeldt, Nora
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Kirdök, Emrah
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Vicente, Mário
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Naidoo, Thijesse ...
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van der Valk, To ...
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Altınışık, N. Ez ...
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Krzewińska, Maja ...
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Dalén, Love, 198 ...
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Götherström, And ...
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Mirabello, Claud ...
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Unneberg, Per
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Oskolkov, Nikola ...
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Stockholm University
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Uppsala University
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Linköping University
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Lund University
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Swedish Museum of Natural History