The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform
Open accessAbstract
Summary: Studying fungal biodiversity using data generated from I llumina M i S eq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables. Here, we introduce PIPITS, an open‐source stand‐alone suite of software for automated processing of I llumina M i S eq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired‐end reads from quality filtering to producing OTU abundance tables. We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the M i S eq platform from I llumina M i S eq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITS x to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.
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QIIME allows analysis of high-throughput community sequencing data
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Towards a unified paradigm for sequence‐based identification of fungi
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Self-citationKalan, L., Loesche, M., Hodkinson, B. P., Heilmann, K., Ruthel, G., Gardner, S. E., & Grice, E. A. (2016) · mBio · doi:10.1128/mbio.01058-16 · Cited by 246
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Sekse, C., Holst-Jensen, A., Dobrindt, U., Johannessen, G. S., Li, W., Spilsberg, B., & Shi, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02029 · Cited by 98
Yadav, A., Wang, Y., Jain, K., Panwar, V. A. R., Kaur, H., Kasana, V., Xu, J., & Chowdhary, A. (2023) · Journal of Fungi · doi:10.3390/jof9070720 · Cited by 38
Metadata
- Authors
- Gweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I., & Schonrogge, K.
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2015-05-25
- Volume
- 6
- Issue
- 8
- Pages
- 973-980
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W1870711663
- Cited by
- 332
- References
- 29
- FWCI
- 18.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- CoChat. (2026). Citation check: PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. https://app.cochat.ai/papers/10.1111/2041-210x.12399
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- Gweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I., & Schonrogge, K. (2015). PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.12399
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