ArticleGigaScience2013
AXIOME: automated exploration of microbial diversity.
Article in GigaScience, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction.Scientific reports · 2021Article
- AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.GigaScience · 2021Article
- Validating DNA Extraction Protocols for Bentonite Clay.mSphere · 2019Article
- Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone.PloS one · 2019Article
- Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors.Microbial ecology · 2017Article
- Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry.Scientific reports · 2017Article
- Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity.NPJ biofilms and microbiomes · 2017Article
- Acidification Enhances Hybrid NFrontiers in microbiology · 2016Article
- Microbial biogeography of a university campus.Microbiome · 2015Article
- Developmental succession of the microbiome of Culex mosquitoes.BMC microbiology · 2015Article
- Article
- Metagenomics: Retrospect and Prospects in High Throughput Age.Biotechnology research international · 2015Review
- Evaluating bias of illumina-based bacterial 16S rRNA gene profiles.Applied and environmental microbiology · 2014Article
- Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.mBio · 2014Article
- Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria.Frontiers in microbiology · 2014Article
- Culture-independence for surveillance and epidemiology.Pathogens (Basel, Switzerland) · 2013Article
- Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance.PloS one · 2013Article
- Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.PloS one · 2013Article
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough 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.
findingsAXIOME streamlines and manages analysis of small 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.
conclusionsAXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.