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AmpliconNoise specifications

Information


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

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Documentation


Publication for AmpliconNoise

AmpliconNoise citations

 (97)
library_books

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare

2018
Sci Rep
PMCID: 5934373
PMID: 29725059
DOI: 10.1038/s41598-018-25450-4

[…] 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 us […]

call_split

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

2018
PMCID: 5880877
PMID: 29611319
DOI: 10.14814/phy2.13649
call_split See protocol

[…] 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 and the s […]

library_books

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

2018
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 […]

library_books

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

2018
Appl Environ Microbiol
PMCID: 5772229
PMID: 29150503
DOI: 10.1128/AEM.01049-17

[…] 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 […]

library_books

16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing

2017
BMC Bioinformatics
PMCID: 5751400
PMID: 29297318
DOI: 10.1186/s12859-017-1975-3

[…] ], as well as MEGAN [] and Mothur []. SILVAngs [] is a web page analysis tool that based on the SILVA database for the OTU species classification, only supports the maximum 500 M sequencing data. And AmpliconNoise [] is mainly used for 454 sequencing data. All these tools are useful and has been used in so many research projects. However, all these tools are focusing on taxonomy assignment and div […]

call_split

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

2017
Front Microbiol
PMCID: 5737034
PMID: 29326666
DOI: 10.3389/fmicb.2017.02503
call_split See protocol

[…] ality-controlled using the split_libraries.py 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 pick_otus.py script (based on 97% sequence similarity). […]

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

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