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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

Versioning


No version available

Maintainer


  • person_outline Chris Quince

Publication for PyroNoise

PyroNoise citations

 (139)
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Killing Effects of an Isolated Serratia marcescens KH 001 on Diaphorina citri via Lowering the Endosymbiont Numbers

2018
Front Microbiol
PMCID: 5938409
PMID: 29765368
DOI: 10.3389/fmicb.2018.00860
call_split See protocol

[…] 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 (). Brief […]

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In feed bambermycin medication induces anti inflammatory effects and prevents parietal cell loss without influencing Helicobacter suis colonization in the stomach of mice

2018
PMCID: 5894178
PMID: 29636083
DOI: 10.1186/s13567-018-0530-1
call_split See protocol

[…] ing 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 sequen […]

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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

[…] s 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. […]

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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

[…] rection 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 con […]

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Bacterial Community of the Rice Floodwater Using Cultivation Independent Approaches

2018
PMCID: 5831270
PMID: 29666650
DOI: 10.1155/2018/6280484
call_split See protocol

[…] zed 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 were […]

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Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease

2018
PLoS One
PMCID: 5785003
PMID: 29370299
DOI: 10.1371/journal.pone.0191884
call_split See protocol

[…] Microbial community sequences were analyzed using the software package Mothur []. Denoising of the raw data was performed with the tool shhh.flows, an adaptation of the PyroNoise algorithm []. Multiplex identifier barcodes and adapters were removed, as well as sequences shorter than 250 bp. bacterial sequences were aligned using the align.seqs tool against the SILVA […]

Citations

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

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