TY  - JOUR
A1  - Bálint, Miklós
A1  - Schmidt, Philipp-André
A1  - Sharma, Rahul
A1  - Thines, Marco
A1  - Schmitt, Imke
T1  - An illumina metabarcoding pipeline for fungi
T2  - Ecology and evolution
N2  - 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.
KW  - community ecology
KW  - data pruning
KW  - high throughput
KW  - internal transcribed spacer rDNA
KW  - next-generation sequencing
Y1  - 2014
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/34801
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-348012
SN  - 2045-7758
N1  - 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.
VL  - 4
IS  - 13
SP  - 2642
EP  - 2653
PB  - John Wiley & Sons, Inc.
CY  - [S.l.]
ER  -