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Open Access AXIOME: automated exploration of microbial diversity
BibTeX
@MISC{Lynch_openaccess,
author = {Michael Dj Lynch and Andre P Masella and Michael W Hall and Andrea K Bartram and Josh D Neufeld},
title = {Open Access AXIOME: automated exploration of microbial diversity},
year = {}
}
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Abstract
Background: Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research. Findings: AXIOMEstreamlinesandmanagesanalysisofsmall subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows. Conclusions: AXIOME is an actively developed, open source project written in Vala and available from GitHub
Keyphrases
automated exploration microbial diversity open access axiome extensible management tool research workflow companion graphical user interface microbial ecology small subunit rrna gene indicator specie analysis illumina sequence high-throughput sequencing marker data popular microbial ecology analysis package non-negative matrix factorization microbial research multi-response permutation procedure open source project phylogenetic novelty paired-end assembler microbial ecosystem
