PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform
Research output: Contribution to journal › Article › peer-review
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DOI
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 language | English |
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Pages (from-to) | 973-980 |
Number of pages | 8 |
Journal | Methods in Ecology and Evolution |
Volume | 6 |
Issue number | 8 |
DOIs | |
Publication status | Published - 22 Apr 2015 |
Externally published | Yes |