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Great differences i...
Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
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- Anslan, Sten (författare)
- Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany
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- Nilsson, R. Henrik, 1976 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden
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- Wurzbacher, Christian, 1980 (författare)
- Tech Univ Munich, Coulombwall 3, D-85748 Garching, Germany
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- Baldrian, Petr (författare)
- Czech Acad Sci, Inst Microbiol, Videnska 1083, Prague 14220 4, Czech Republic
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- Tedersoo, Leho (författare)
- Tartu Univ, Nat Hist Museum, 14a Ravila, Tartu 50411, Estonia
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- Bahram, Mohammad (författare)
- Uppsala universitet,Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för ekologi,Department of Ecology,University of Tartu,Uppsala University,Systematisk biologi,Tartu Univ, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden
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(creator_code:org_t)
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- 2018-09-10
- 2018
- Engelska.
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 39, s. 29-40
- Relaterad länk:
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https://mycokeys.pen...
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https://doi.org/10.3...
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https://uu.diva-port... (primary) (Raw object)
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https://gup.ub.gu.se...
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https://doi.org/10.3...
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https://res.slu.se/i...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.
Ämnesord
- NATURVETENSKAP -- Biologi -- Annan biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Other Biological Topics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Annan naturvetenskap (hsv//swe)
- NATURAL SCIENCES -- Other Natural Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
Nyckelord
- Amplicon sequencing
- Fungal biodiversity
- Metagenomics
- Microbial communities
- Microbiome
- Mycobiome
- Microbial communities
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