| Registro completo |
| Provedor de dados: |
Nature Precedings
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| País: |
United Kingdom
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| Título: |
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0
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| Autores: |
James R. White
Cesar Arze
Malcolm Matalka
The CloVR Team
Owen White
Samuel V. Angiuoli
W. Florian Fricke
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| Data: |
2011-10-12
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| Ano: |
2011
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| Palavras-chave: |
Ecology
Genetics & Genomics
Microbiology
Bioinformatics
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| Resumo: |
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:

A) Mothur – a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);
B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;
C) Qiime – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac) for within-(alpha diversity) and between-(beta diversity) sample analysis;
D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.

Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyro-tagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.
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| Tipo: |
Manuscript
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| Identificador: |
http://precedings.nature.com/documents/5888/version/3
oai:nature.com:10.1038/npre.2011.5888.3
http://dx.doi.org/10.1038/npre.2011.5888.3
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| Fonte: |
Nature Precedings
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| Direitos: |
Creative Commons Attribution 3.0 License
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