PyNAST protocols

PyNAST specifications

Information


Unique identifier OMICS_15419
Name PyNAST
Alternative names Python Nearest Alignment Space Termination, NAST, Nearest Alignment Space Termination
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.2.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rob Knight <>

Publication for Python Nearest Alignment Space Termination

PyNAST IN pipelines

 (25)
2018
PMCID: 5768916
PMID: 29375529
DOI: 10.3389/fmicb.2017.02667

[…] al., 2012) with a minimum identity of 97%. taxonomy was assigned using uclust (version 1.2.22) (edgar, 2010) with the greengenes database as reference (version 13.8) and sequences were aligned using pynast (version 1.2.2) (caporaso et al., 2010a). otu’s identified in less than 0.1% of the reads were removed as well as reads identified as chloroplast or mitochondria. archaea were not filtered […]

2018
PMCID: 5826226
PMID: 29515550
DOI: 10.3389/fmicb.2018.00270

[…] taxonomic units using the pick_open_reference_otus.py command with default parameters using the uclust method (edgar, 2010). otus occurring only once (singletons) or that failed to align using pynast were removed (caporaso et al., 2010a). relative diversity analyses were generated using the command core_diversity_analyses.py. raw sequence reads have been submitted to the sequence read […]

2018
PMCID: 5835065
PMID: 29535685
DOI: 10.3389/fmicb.2018.00280

[…] (edgar, 2013) and the dereplicated reads were clustered into otus at a 97% sequence similarity threshold. singleton otus were removed and the remaining high-quality sequence reads were aligned with pynast (caporaso et al., 2010a) against the ribosomal database project (rdp, release 11.3)., based on the growth profiles of the cultures, three time series samples (days 1, 3, and 5) were collected […]

2017
PMCID: 5313486
PMID: 28261182
DOI: 10.3389/fmicb.2017.00226

[…] similarity using an open reference otu picking strategy. the most abundant sequence in each otu was selected as representative sequences and further aligned against the greengenes core set using pynast software (caporaso et al., 2010). taxonomy was assigned to each otu using the ribosomal database project (rdp) classifier with a minimum confidence threshold of 80% (wang et al., 2007). […]

2017
PMCID: 5317032
PMID: 28218290
DOI: 10.1038/srep42625

[…] reads using the uclust61 with a pairwise identity threshold of 0.97., representative sequences for each otu were picked using the “most–abundant” method and otu sequence alignment was performed with pynast59. the ribosomal database project (rdp)62 classifier was used for taxonomic assignment with a 95% confidence threshold. sequences with the best match for eukaryotes (i.e. chloroplasts […]

PyNAST institution(s)
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA; Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
PyNAST funding source(s)
This work was funded in part by grants T15LM009451; a Bill and Melinda Gates Foundation Mal-ED Network Discovery Project; 1U01HG004866-01; Human Microbiome Demonstration project grant UH2DK083981; from Human Microbiome Project of the NIH Roadmap Initiative and National Cancer Institute grant UH2CA140233.

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