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AmpliconNoise specifications


Unique identifier OMICS_01112
Name AmpliconNoise
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


Publication for AmpliconNoise

AmpliconNoise citations


Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare

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

[…] 454 life sciences) at the university of poitiers (france)., the 16s rrna gene pyrotags were analysed using qiime version 1.9.1 and r (r project 3.3.2). briefly, the flowgrams were denoised with ampliconnoise, and chimeras were removed using perseus. all reads shorter than 250 bp were discarded and the remaining reads were clustered into operational taxonomic units (otus) at 97% similarity […]


Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans

PMCID: 5880877
PMID: 29611319
DOI: 10.14814/phy2.13649

[…] and agarose gel electrophoresis of a standard pcr reaction using each primer set, the same cycling conditions and dna template., the sequences were processed in qiime (caporaso et al. ) using the ampliconnoise (quince et al. ) pipeline that utilizes flowgram information of the sequences to correct for errors. the samples were demultiplexed by exact matching of both barcode and primer […]


Analytical parameters and validation of homopolymer detection in a pyrosequencing based next generation sequencing system

BMC Genomics
PMCID: 5822529
PMID: 29466940
DOI: 10.1186/s12864-018-4544-x

[…] ols to separate artifacts from true genetic variations. some of these algorithms are based on clustering the flowgrams; for example denoiser, which utilizes rank-abundance distributions, or pyronoise/ampliconnoise, which calculates a likelihood using empirically derived error distributions []. acacia’s main focus is on hp sequences and the algorithm uses a dynamically updated cluster consensus whe […]


Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments

Appl Environ Microbiol
PMCID: 5772229
PMID: 29150503
DOI: 10.1128/AEM.01049-17

[…] gene sequences are available from mg-rast with the accession numbers mgm4758641.3 to mgm4758688.3., the 16s rrna amplicon sequences were analyzed in mothur (v. 1.26) (), qiime (v. 1.5.0) (), and ampliconnoise (v.1.24) (). all samples were passed through the ampliconnoise pipeline to remove both sequencing and pcr errors and chimeras with its perseus algorithm and trimmed to 250 bp. sequences […]


Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

Front Microbiol
PMCID: 5737034
PMID: 29326666
DOI: 10.3389/fmicb.2017.02503

[…] using the with following settings: 200 < sequence length < 1,000, mean quality > 25, ambiguous bases < 1, and homopolymer length < 6. sequences were denoised using ampliconnoise algorithm (shhh.seqs) in mothur v.1.33.3 (schloss et al., ; quince et al., ; liu et al., ). the sequences were then analyzed using script (based on 97% sequence […]


Soil Conditions Rather Than Long Term Exposure to Elevated CO2 Affect Soil Microbial Communities Associated with N Cycling

Front Microbiol
PMCID: 5651278
PMID: 29093701
DOI: 10.3389/fmicb.2017.01976

[…] to barcode labeled 454 pyrosequencing (gatc, köln, germany)., sequence processing and analysis was done in qiime 1.3 ( pyrosequencing and pcr errors of the reads were corrected using the ampliconnoise pipeline (quince et al., ). sequences of functional marker genes (nirk/nirs, nosz, archaeal and bacterial amoa, nifh, and nrfa) were clustered as described previously (caporaso et al., […]

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AmpliconNoise institution(s)
Department of Civil Engineering, University of Glasgow, Rankine Building, Glasgow, UK

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