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PIPITS : an automated pipeline for analyses of fungal internal transcribed spacer sequences from the I llumina sequencing platform
Author(s) -
Gweon Hyun S.,
Oliver Anna,
Taylor Joanne,
Booth Tim,
Gibbs Melanie,
Read Daniel S.,
Griffiths Robert I.,
Schonrogge Karsten
Publication year - 2015
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12399
Subject(s) - pipeline (software) , computer science , computational biology , biology , programming language
Summary Studying fungal biodiversity using data generated from I llumina M i S eq 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 I llumina M i S eq 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 M i S eq platform from I llumina M i S eq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITS x to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.