Grinder specifications

Information


Unique identifier OMICS_01508
Name Grinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Grinder

Grinder in publications

 (8)
PMCID: 5215245
PMID: 28052134
DOI: 10.1371/journal.pone.0169563

[…] taxa []. those two pairs of primers cover 82.1% and 83% of the bacterial domain for 200(v3) and 400(v4-v5) respectively, according to testprime (klindworth, 2012) on the silva ssu r122 database., grinder [] was used to extract amplicons from complete genomic sequences. this software fetches amplicons randomly across the several potential 16s rdna copies within a genome sequence. simulated […]

PMCID: 4844954
PMID: 27112993
DOI: 10.1038/srep24965

[…] then, since the uparse bioinformatics pipeline has only been validated for microbes (bacteria and fungi), we validated the pipeline by simulating reads from mock arthropod communities using grinder v.0.5.3 and processing the simulated data with usearch v.8.153. we downloaded a coi reference database of 3,306,508 arthropod sequences from the barcode of life database (bold). we then used […]

PMCID: 4649493
PMID: 26576508
DOI: 10.1038/srep16814

[…] information criterion to study the change in bacterial community richness and evenness., to ensure our pipeline can perform sensitive and specific mapping, we employed a shotgun sequence simulator, grinder (http://sourceforge.net/projects/biogrinder/) to generate two sets of artificial human, bovis, mouse and yeast transcriptome data under 0 or 2 mismatch allowance. the human, bovis and mouse […]

PMCID: 4493402
PMID: 26217378
DOI: 10.3389/fgene.2015.00235

[…] it is also important to model bqs. however, some read simulators do not provide quality scores, e.g., metasim (), celsim (), and gensim (). alternatively, fixed quality values are generated by grinder (). correct bases are assigned a quality score of 30 and error positions are assigned a score of 10. the pirs by uses quality scores from an existing sequence dataset. while this approach […]

PMCID: 3970189
PMID: 24682077
DOI: 10.1038/srep04516

[…] were selected at random. an overview of the organisms, the respective genome size and %gc of each genome can be found in (online). sequence fragments of specific lengths were generated using grinder. the following parameters were used: -rd 1000 normal 0 -cf 1, while also applying different lengths for the sequences, e.g. -rd 800, to assess the separation of groups based on the sequence […]


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Grinder institution(s)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia

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