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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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Publication for AmpliconNoise

AmpliconNoise in pipelines

 (5)
2017
PMCID: 5572350
PMID: 28878691
DOI: 10.3389/fphys.2017.00615

[…] sequences was carried out using the mothur analysis suite v1.34.0 (schloss et al., ) based on the schloss standard operating procedure (sop) (schloss et al., ). sequences were first de-noised using ampliconnoise algorithm (quince et al., ) as implemented by mother. after de-noising, any sequences that were <400 bp in length and/or had one of the following: >2 mismatches in the primer, […]

2015
PMCID: 4345813
PMID: 25784904
DOI: 10.3389/fmicb.2015.00167

[…] based on the 5 bp sample-specific barcodes and processed to remove poor-quality sequences. to reduce sequencing errors, the shhh.flows command was applied, which is the mothur implementation of the ampliconnoise algorithm (quince et al., ). quality filters were applied to trim and remove sequences with the following characteristics: less than 200 bp in length; average quality score less […]

2014
PMCID: 4260508
PMID: 25538699
DOI: 10.3389/fmicb.2014.00689

[…] mothur v.1.33.3 (schloss et al., ) with default command parameters, unless specified. flowgrams were trimmed to 450 flows and de-noised using the shhh.flows command, the mothur implementation of the ampliconnoise algorithm (quince et al., ). the resulting sequences were trimmed (pdiffs = 2, bdiffs = 0, maxhomop = 6, minlength = 250) followed by alignment against the silva 16s rrna gene reference […]

2013
PMCID: 3543377
PMID: 23326555
DOI: 10.1371/journal.pone.0053987

[…] mothur v1.21.1 . clusters delimited at these 6 grammatical threshold levels with gramcluster are available in . we also clustered forward sequences that were quality-trimmed, but not processed with ampliconnoise at 97% threshold to evaluate the effects of the data pruning step on the recovered cluster numbers., we analyzed fungal community structures by selecting all blast hits assignable […]

2012
PMCID: 3390581
PMID: 22783228
DOI: 10.3389/fmicb.2012.00172

[…] and regions of the 16s rrna gene provided good technical replication for these samples., barcoded reads were processed using mothur: the data were denoised using the mothur implementation of the ampliconnoise algorithm (quince et al., ), barcodes and primers were removed, sequences were aligned to the silva database and filtered, chimeras were detected using uchime and removed, […]

AmpliconNoise in publications

 (92)
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 […]

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 […]

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 […]

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 […]

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

[…] 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 […]

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

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