An illumina metabarcoding pipeline for fungi
- High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
Author: | Miklós BálintORCiDGND, Philipp-André SchmidtORCiDGND, Rahul SharmaGND, Marco ThinesORCiDGND, Imke SchmittORCiDGND |
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URN: | urn:nbn:de:hebis:30:3-348012 |
DOI: | https://doi.org/10.1002/ece3.1107 |
ISSN: | 2045-7758 |
Pubmed Id: | https://pubmed.ncbi.nlm.nih.gov/25077016 |
Parent Title (German): | Ecology and evolution |
Publisher: | John Wiley & Sons, Inc. |
Place of publication: | [S.l.] |
Document Type: | Article |
Language: | English |
Date of Publication (online): | 2014/08/08 |
Date of first Publication: | 2014/06/02 |
Publishing Institution: | Universitätsbibliothek Johann Christian Senckenberg |
Release Date: | 2014/08/08 |
Tag: | community ecology; data pruning; high throughput; internal transcribed spacer rDNA; next-generation sequencing |
Volume: | 4 |
Issue: | 13 |
Page Number: | 12 |
First Page: | 2642 |
Last Page: | 2653 |
Note: | Copyright © 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
HeBIS-PPN: | 450966690 |
Institutes: | Biowissenschaften / Biowissenschaften |
Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft | |
Biowissenschaften / Institut für Ökologie, Evolution und Diversität | |
Fachübergreifende Einrichtungen / Biodiversität und Klima Forschungszentrum (BiK-F) | |
Dewey Decimal Classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Sammlungen: | Universitätspublikationen |
Sammlung Biologie / Sondersammelgebiets-Volltexte | |
Licence (German): | Creative Commons - Namensnennung 4.0 |