Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
Journal article, 2012

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.




sequence quality control

sequence reliability



R. Henrik Nilsson

University of Gothenburg

Leho Tedersoo

Kessy Abarenkov

Martin Ryberg

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Martin Hartmann

Conrad L. Schoch

Johan A. A. Nylander

Johannes Bergsten

Teresita M. Porter

Ari Jumpponen

Parag Vaishampayan

Otso Ovaskainen

Nils Hallenberg

University of Gothenburg

Johan Bengtsson

University of Gothenburg

Martin Eriksson

University of Gothenburg

Karl-Henrik Larsson

Ellen Larsson

University of Gothenburg

Urmas Kõljalg


1314-4057 (ISSN) 1314-4049 (eISSN)

Vol. 4 37-63

Subject Categories


Biological Systematics

Soil Science



Microbiology in the medical area

Bioinformatics and Systems Biology



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