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Denoising software tools | 16S ribosomal RNA sequencing data analysis

In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR…
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Denoiser
Desktop

Denoiser

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance…

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

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Acacia
Desktop

Acacia

An error-corrector for pyrosequenced amplicon reads. Acacia reduces the number…

An error-corrector for pyrosequenced amplicon reads. Acacia reduces the number and complexity of alignments. Rather than performing all-against-all alignments in a cluster, each read in the cluster…

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PyroNoise
Desktop

PyroNoise

Clusters the flowgrams of 454 pyrosequencing reads using a distance measure…

Clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. PyroNoise is not restricted to…

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DADA
Desktop

DADA Divisive Amplicon Denoising Algorithm

Corrects amplicon errors without constructing Operational Taxonomic Units…

Corrects amplicon errors without constructing Operational Taxonomic Units (OTUs). DADA2 is an R package that implements a quality-aware model of Illumina amplicon errors. This application is…

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mothur
Desktop

mothur

Aims to be a comprehensive software package that allows users to use a single…

Aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. mothur builds upon previous tools to provide a flexible and…

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AmpliconNoise
Desktop

AmpliconNoise

AmpliconNoise is a collection of programs for the removal of noise from 454…

AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.

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HECTOR
Desktop

HECTOR

A parallel multistage homopolymer spectrum based error corrector for 454…

A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. HECTOR employs a multi-threaded design based on a master-slave computing model. It is a practical 454…

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MeFiT
Desktop

MeFiT Merging and Filtering Tool for Paired-End Reads

A python pipeline to merge and filter paired end Illumina reads. MeFiT performs…

A python pipeline to merge and filter paired end Illumina reads. MeFiT performs following two steps: (i) merging of overlapping paired-end sequences, and (ii)filtering data for quality. MeFiT can be…

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IPED
Desktop

IPED

A powerful denoising tool for correcting sequencing errors in Illumina MiSeq…

A powerful denoising tool for correcting sequencing errors in Illumina MiSeq 16S rRNA gene amplicon sequencing data. IPED includes a machine learning method which predicts potentially erroneous…

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FlowClus
Desktop

FlowClus

Uses a systematic approach to filter and denoise reads efficiently. When…

Uses a systematic approach to filter and denoise reads efficiently. When denoising real datasets, FlowClus provides feedback about the process that can be used as the basis to adjust the parameters…

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NoDe
Desktop

NoDe Noise Detector

An error correction algorithm trains to identify positions in 454 sequencing…

An error correction algorithm trains to identify positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in…

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FunFrame
Desktop

FunFrame

Uses algorithms to de-noise functional gene pyrosequences and performs…

Uses algorithms to de-noise functional gene pyrosequences and performs ecological analysis on de-noised sequence data. FunFrame is an R-based data-analysis pipeline which provides users a unified set…

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PyroClean
Desktop

PyroClean

Denoises homopolymers from pyrosequence technologies. PyroClean has been…

Denoises homopolymers from pyrosequence technologies. PyroClean has been designed for protein-coding gene regions that are evolutionarily conserved with regard to amino acid composition and…

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KEC
Desktop

KEC K-mer-based Error Correction

An efficient error correction algorithm optimized for viral amplicons. KEC is…

An efficient error correction algorithm optimized for viral amplicons. KEC is highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous…

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