Electronic versions

DOI

  • Hyun S. Gweon
  • Anna Oliver
  • Joanne Taylor
  • Tim Booth
  • Melanie Gibbs
  • Daniel S. Read
  • Robert I. Griffiths
    Centre for Ecology and Hydrology, Wallingford
  • Karsten Schonrogge
Summary 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.

Keywords

  • bioinformatics, DNA metabarcoding, fungi, internal transcribed spacer, pipeline
Original languageEnglish
Pages (from-to)973-980
Number of pages8
JournalMethods in Ecology and Evolution
Volume6
Issue number8
DOIs
Publication statusPublished - 22 Apr 2015
Externally publishedYes
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