ArticleMethods in ecology and evolution2015
PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.
Article in Methods in ecology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers, 1 of them a synthesis that pooled it.
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140 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.Molecular ecology resources · 2025Article
- Pomegranate Woody Mycobiota Associated with Wood Decay.Journal of fungi (Basel, Switzerland) · 2025Article
- Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa.Applied and environmental microbiology · 2025Article
- Dynamics and Insights into the Unique Ecological Guild of Fungi in Bacteria-Bioaugmented Anaerobic Digesters.Journal of fungi (Basel, Switzerland) · 2025Article
80 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Studying fungal biodiversity using data generated from Illumina MiSeq 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 Illumina MiSeq 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 MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx 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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