PyNAST protocols

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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

 (175)
2018
PMCID: 5762819
PMID: 29321642
DOI: 10.1038/s41598-017-18348-0

[…] of smrt portal version 2.7 (pacific biosciences). high-quality sequences were extracted using the quantitative insights into microbial ecology (qiime) package (version 1.7) and aligned by pynast and uclust under 100% clustering of sequence identity to obtain representative sequences. the unique sequence set was classified into otus under 98.6% threshold identity using uclust. […]

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

[…] 2.0) method () with a minimum identity of 97%. taxonomy was assigned using uclust (version 1.2.22) () with the greengenes database as reference (version 13.8) and sequences were aligned using pynast (version 1.2.2) (). 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 out. picrust (version […]

2018
PMCID: 5789842
PMID: 29382896
DOI: 10.1038/s41598-018-20302-7

[…] obtained through each step is reported in table . high-quality amplicon reads were subsequently analysed by the qiime pipeline, aligning them against the silva database (v119) by means of the pynast aligner using the open-reference strategy and clustering them at 97% of identity. the chimeraslayer tool was used to assess the presence of chimeric sequences, which were not found […]

2018
PMCID: 5793709
PMID: 29404208
DOI: 10.7717/peerj.4272

[…] taxonomic units (otus) were generated for the remaining sequences based on a 97% sequence similarity with the uclust method (). the representative sequences were picked for each otu, aligned using pynast (), and assigned into taxonomic groups against the greengenes database v.13.8 (). construction of phylogenic tree was conducted with the program fasttree (). the otus assigned into archaea, […]

2018
PMCID: 5799165
PMID: 29402949
DOI: 10.1038/s41598-018-20508-9

[…] abundant sequence in each otu. representative sequences (at 97% similarity) were then classified taxonomically using ribosomal database project (rdp) classifier 2.0.1. the otus were aligned using pynast with a minimum alignment length of 150 bp and a minimum percent identity of 75%. after alignment, ph lane mask (http://greengenes.lbl.gov/) was conducted to screen out the hypervariable […]


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PyNAST in publications

 (722)
PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18

[…] lower than 20 were removed. chimeric sequences were checked and removed using usearch version 6.1.544 (). the remaining high-quality reads were clustered into operational taxonomic units (otus) by pynast () with a 97% sequence identity threshold against the greengenes core set database version 13.8 (). the generated biome table was normalized using an equal subsampling size of 2,938 sequences. […]

PMCID: 5942802
PMID: 29742123
DOI: 10.1371/journal.pone.0196178

[…] quality filtering, qiime default parameters were used, with a minimun phred quality score <20 and ambiguous nucleotides were removed. sequence alignment was made using greengenes database [] and pynast alignment algorithm []. uclust software [] was used to assign similar sequences to operational taxonomic units (otus) by clustering sequences based on a 97% similarity threshold. the taxonomic […]

PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] as part of the pick_open_reference_otus.py workflow, representative sequences from each otu were selected and aligned against the greengenes database gg_13_8 preclustered at 85% identity using pynast [] and used to build a tree using fasttree []. the otu matching to chloroplasts of plant origin (“streptophyta”) based on greengenes taxonomic classification was manually removed. to improve […]

PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] similarity threshold of 97% (roughly corresponding to species-level otus). representative sequences from the otus were aligned to a pre-aligned database of sequences (the greengenes core set) using pynast with quality thresholds set with a minimum sequence length of 150 nucleotides and a minimum percent identity of 75%. pynast alignment failures were investigated by blasting all sequences […]

PMCID: 5934373
PMID: 29725059
DOI: 10.1038/s41598-018-25450-4

[…] reads were clustered into operational taxonomic units (otus) at 97% similarity using uclust. representative sequences were aligned against the silva reference alignment (release 108,) using pynast and identified using the rdp classifier. rare otus (i.e. singletons and doubletons) were discarded, resulting in 1380 otus represented by ≥3 reads (see supplementary table  for details). […]


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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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