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Five simple guideli...
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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Tedersoo, Leho (author)
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Abarenkov, Kessy (author)
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Ryberg, Martin, 1976 (author)
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
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Hartmann, Martin (author)
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Schoch, Conrad L. (author)
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Nylander, Johan A. A. (author)
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Bergsten, Johannes (author)
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Porter, Teresita M. (author)
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Jumpponen, Ari (author)
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Vaishampayan, Parag (author)
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Ovaskainen, Otso (author)
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- Hallenberg, Nils, 1947 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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- Bengtsson-Palme, Johan, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg
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- Eriksson, Martin, 1970 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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Larsson, Karl-Henrik, 1948 (author)
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- Larsson, Ellen, 1961 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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Kõljalg, Urmas (author)
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Schoch, G. (author)
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(creator_code:org_t)
- 2012-09-05
- 2012
- English.
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Abstract
Subject headings
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- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
Subject headings
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
Keyword
- ITS
- sequence reliability
- sequence quality control
- fungi
- databases
- barcoding
- barcoding
Publication and Content Type
- ref (subject category)
- art (subject category)
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Nilsson, R. Henr ...
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Tedersoo, Leho
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Abarenkov, Kessy
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Ryberg, Martin, ...
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Kristiansson, Er ...
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Hartmann, Martin
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Schoch, Conrad L ...
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Nylander, Johan ...
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Bergsten, Johann ...
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Porter, Teresita ...
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Jumpponen, Ari
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Vaishampayan, Pa ...
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Ovaskainen, Otso
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Hallenberg, Nils ...
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Bengtsson-Palme, ...
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Eriksson, Martin ...
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Larsson, Karl-He ...
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Larsson, Ellen, ...
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Kõljalg, Urmas
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Schoch, G.
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MycoKeys
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University of Gothenburg
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Chalmers University of Technology
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Uppsala University