title: PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.
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.
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Hyun S
authors: HS
authors: Gweon
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Anna
authors: A
authors: Oliver
authors: Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR UK.
authors: Joanne
authors: J
authors: Taylor
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Tim
authors: T
authors: Booth
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Melanie
authors: M
authors: Gibbs
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Daniel S
authors: DS
authors: Read
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Robert I
authors: RI
authors: Griffiths
authors: Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK.
authors: Karsten
authors: K
authors: Schonrogge
keywords: DNA metabarcoding; bioinformatics; fungi; internal transcribed spacer; pipeline