PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

Gweon, Hyun S. ORCID: https://orcid.org/0000-0002-6218-6301; Oliver, Anna; Taylor, Joanne; Booth, Tim; Gibbs, Melanie ORCID: https://orcid.org/0000-0002-4091-9789; Read, Daniel S. ORCID: https://orcid.org/0000-0001-8546-5154; Griffiths, Robert I. ORCID: https://orcid.org/0000-0002-3341-4547; Schonrogge, Karsten ORCID: https://orcid.org/0000-0003-0122-6493. 2015 PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution, 6 (8). 973-980. 10.1111/2041-210X.12399

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Abstract/Summary

1. 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. 2. 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. 3. 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. 4. 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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1111/2041-210X.12399
UKCEH and CEH Sections/Science Areas:	Acreman Pywell Rees (from October 2014)
ISSN:	2041-210X
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link.
Additional Keywords:	bioinformatics, DNA metabarcoding, fungi, internal transcribed spacer, pipeline
NORA Subject Terms:	Ecology and Environment
Date made live:	07 Jul 2015 14:24 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/511230

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