PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform
Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid
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Yn: Methods in Ecology and Evolution, Cyfrol 6, Rhif 8, 22.04.2015, t. 973-980.
Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid
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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 -