PyroNoise protocols

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PyroNoise specifications

Information


Unique identifier OMICS_08901
Name PyroNoise
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Roche
Operating system Unix/Linux
Parallelization MPI
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Chris Quince <>

Publication for PyroNoise

PyroNoise in pipelines

 (17)
2017
PMCID: 5372479
PMID: 28386469
DOI: 10.1556/1886.2016.00040

[…] technology either at institute of microbiology and genetics, georg-august university göttingen, göttingen, germany or at eurofins genomics, ebersberg, germany. the data were then processed using the pyronoise implementation in mothur v. 1.36.1 []. all sequences have been deposited at ncbi with the project number prjna347641. the sequence reads were aligned to all the known sts in the slst […]

2017
PMCID: 5488102
PMID: 28587211
DOI: 10.3390/microorganisms5020031

[…] following manufacturer’s guidelines. sequencing raw data were processed using mothur v.1.33.0 []. the flowgrams of each sample were distinguished according to their tag and were denoised with the pyronoise software []. after removing primer sequences, tag, and key fragments, only sequences with ≥200 bp having homopolymers <8 bp were kept for further analysis. chimeras were recognised using […]

2017
PMCID: 5605529
PMID: 28928412
DOI: 10.1038/s41598-017-11552-y

[…] software was used to analyze the pyrosequencing data following schloss et al. standard operation procedure (454 sop). briefly, all sequences were denoised using the mothur’s implementation of the pyronoise algorithm. sequences with more than two mismatch bases in the primers, one mismatched base in the barcode and homologous bases longer than 8 bp were discarded. sequence reads were aligned […]

2017
PMCID: 5605657
PMID: 28928457
DOI: 10.1038/s41598-017-11244-7

[…] sop for 454 data. the flowgrams were demultiplexed (mismatch barcode:2, mismatchprimer:3, size: 390 bp) and corrected using the shhh.flows command, which is the mothur implementation of the original pyronoise algorithm. the sequences were aligned to the bacterial reference alignment (http://www.mothur.org/wiki/silva_reference_alignment) which is based on the silva 119 release of the ssuref […]

2016
PMCID: 4731509
PMID: 26858698
DOI: 10.3389/fmicb.2016.00017

[…] laboratory, woods hole, ma, usa. the sequences were submitted to a rigorous quality control procedure based on mothur v24 (), which includes denoising of the flow grams using an algorithm based on pyronoise (), single-linkage preclustering () and removal of pcr errors and a chimera check using uchime (). archaeal and bacterial sequences longer than 79 and 74 bases, respectively, were clustered […]


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PyroNoise in publications

 (144)
PMCID: 5938409
PMID: 29765368
DOI: 10.3389/fmicb.2018.00860

[…] accession no. sub3652522). pcr reactions, pyrosequencing of the pcr amplicons and quality control of raw data were performed as described previously (), to eliminate the low-quality sequences, pyronoise algorithm in mothur (version 1.33.3) were used (), and the quantitative insights into microbial ecology (qiime) platform (version 1.8.0) was implemented for bioinformatics analysis (). […]

PMCID: 5894178
PMID: 29636083
DOI: 10.1186/s13567-018-0530-1

[…] was performed using the roche gs-junior genome sequencer as described previously by rodriguez et al. []. the obtained 16s rrna sequence reads were processed using mothur (software package v1.35), pyronoise algorithm and uchime algorithm for alignment and clustering, denoising and chimera detection, respectively [, ]. the obtained read sets were compared to a reference dataset of aligned […]

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

[…] filtered and trimmed based on identification of low‐quality signals (quince et al. ). the filtered flowgrams were clustered to remove platform‐specific errors and converted into sequences using the pyronoise algorithm. the sequences had barcodes and degenerate primers removed prior to trimming at 500 base pairs (bp). they were then further clustered by seqnoise to remove pcr single base errors. […]

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

[…] tools 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 […]

PMCID: 5831270
PMID: 29666650
DOI: 10.1155/2018/6280484

[…] using the mothur pipeline (version 1.32.1) []. in brief, flowgrams were demultiplexed using the trim.flows command and denoised using the shhh.flows command, which is the mothur implementation of pyronoise []. in addition, adapters, barcodes, primers, short reads, and reads containing more than eight homopolymer bases were removed from the dataset with trim.seqs command. cleaned sequences […]


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

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