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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

Standard Standard

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. / Gweon, Hyun S.; Oliver, Anna; Taylor, Joanne et al.
In: Methods in Ecology and Evolution, Vol. 6, No. 8, 22.04.2015, p. 973-980.

Research output: Contribution to journal › Article › peer-review

HarvardHarvard

Gweon, HS, Oliver, A, Taylor, J, Booth, T, Gibbs, M, Read, DS, Griffiths, RI & 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, vol. 6, no. 8, pp. 973-980. https://doi.org/10.1111/2041-210X.12399

APA

Gweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I., & 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), 973-980. https://doi.org/10.1111/2041-210X.12399

CBE

Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, 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):973-980. https://doi.org/10.1111/2041-210X.12399

MLA

Gweon, Hyun S. et al. "PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform". Methods in Ecology and Evolution. 2015, 6(8). 973-980. https://doi.org/10.1111/2041-210X.12399

VancouverVancouver

Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS et al. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution. 2015 Apr 22;6(8):973-980. doi: 10.1111/2041-210X.12399

Author

Gweon, Hyun S. ; Oliver, Anna ; Taylor, Joanne et al. / PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. In: Methods in Ecology and Evolution. 2015 ; Vol. 6, No. 8. pp. 973-980.

RIS

TY - JOUR

T1 - PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

AU - Gweon, Hyun S.

AU - Oliver, Anna

AU - Taylor, Joanne

AU - Booth, Tim

AU - Gibbs, Melanie

AU - Read, Daniel S.

AU - Griffiths, Robert I.

AU - Schonrogge, Karsten

N1 - https://doi.org/10.1111/2041-210X.12399

PY - 2015/4/22

Y1 - 2015/4/22

N2 - 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.

AB - 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.

KW - bioinformatics

KW - DNA metabarcoding

KW - fungi

KW - internal transcribed spacer

KW - pipeline

U2 - 10.1111/2041-210X.12399

DO - 10.1111/2041-210X.12399

M3 - Article

VL - 6

SP - 973

EP - 980

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

IS - 8

ER -