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

Gweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I. and Schonrogge, K. (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). pp. 973-980. ISSN 2041-210X

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To link to this item DOI: 10.1111/2041-210X.12399

Abstract/Summary

1. Studying fungal biodiversit y 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 o pen-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS e xploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables. 3. We pro vide 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 curatedUNITE fungal data set.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences > Ecology and Evolutionary Biology
ID Code:73815
Publisher:Wiley-Blackwell

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