NAST-iEr statistics

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NAST-iEr specifications

Information


Unique identifier OMICS_16933
Name NAST-iEr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Java, Perl
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Brian Haas <>

Publication for NAST-iEr

NAST-iEr in publications

 (4)
PMCID: 4684203
PMID: 26683192
DOI: 10.1371/journal.pone.0145453

[…] residues, or shorter than minimum length (< 300 nucleotides) were discarded. chimera screening was performed using the chimeraslayer tool, which requires that sequences be previously aligned with nast-ier (hass bj 2011). putative chimeras and other sequences that could not be aligned by nast-ier were removed from subsequent analyses. genus-level taxonomic calls were produced by the rdp […]

PMCID: 4471099
PMID: 26083474
DOI: 10.1371/journal.pone.0128064

[…] bacterial cm model were removed from all subsequent analyses. chimera screening was performed using the software chimeraslayer, which requires that sequences be previously aligned with the software nast-ier.[] putative chimeras and other sequences that could not be aligned by nast-ier were removed from subsequent analyses., genus-level taxonomic classifications were produced by the rdp […]

PMCID: 3745799
PMID: 23337890
DOI: 10.1038/jid.2013.21

[…] method., base calling and quality was determined with phred (; ). bidirectional reads were assembled and aligned to a core set of nast-formatted sequences (rrna16s.gold) using amoscmp16spipeline and nast-ier. suspected chimeras were identified using chimeraslayer and wigeon (). 16s rdna sequences were extensively manually examined. chromatograms were visually inspected at all bases with a phred […]

PMCID: 3374619
PMID: 22720093
DOI: 10.1371/journal.pone.0039315

[…] reads were oriented such that all sequences begin with the 5-prime end according to standard sense strand conventions., for detection of chimeric sequences, all 16s rdna sequences were aligned using nast-ier to obtain a fixed-width alignment, and subjected to cslayer and wigeon . note that for all these tools, we used the original implementation made available […]


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NAST-iEr institution(s)
Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; The Genome Center, Washington University School of Medicine, St. Louis, MI, USA; Human Genomic Medicine, J. Craig Venter Institute, Rockville, MA, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CA, USA
NAST-iEr funding source(s)
This work was supported by NIH with awards to the Baylor College of Medicine (grants U54-HG003273 and U54- HG004973), the Broad Institute (grant U54-HG004969 and NIAID contract HHSN27220090018C), the J. Craig Venter Institute (NIAID contract N01-AI30071 and grant U54-AI084844), Washington University (grants U54-HG003079 and U54-HG004968), and NIH common fund contract U01-HG004866.

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