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Updated: Oct 4, 2025
11:15
Applications of EEG Neuroimaging Data: Event-related Potentials, Spectral Power, and Multiscale Entropy
Published on: June 27, 2013
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DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets.
Adrià Antich1, Creu Palacín2, Xavier Turon1
1Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB- CSIC), Blanes (Girona), Catalonia, Spain.
Peerj
|February 3, 2022
Summary
DnoisE is a new denoising program for DNA metabarcoding that accurately merges erroneous reads with correct ones using codon entropy. This open-source tool enhances biodiversity studies using coding markers like COI and RuBisCO.
Area of Science:
- Genomics
- Bioinformatics
- Ecology
Background:
- DNA metabarcoding is crucial for biodiversity assessment across diverse taxa.
- Amplification and sequencing errors in metabarcoding data can compromise results.
- Existing denoising tools are primarily designed for non-coding ribosomal DNA, not coding markers.
Purpose of the Study:
- To develop a novel denoising program, DnoisE, for coding DNA barcodes used in metabarcoding.
- To address the limitations of current denoising software for markers like COI and RuBisCO.
- To improve the accuracy and reliability of DNA metabarcoding data analysis.
Main Methods:
- Developed DnoisE, an open-source software based on a modified UNOISE algorithm.
- Incorporated codon position variability (entropy) to identify and merge erroneous reads.
- Implemented optional merging strategies and user-supplied codon entropy data.
- Designed the algorithm for parallel processing to reduce computational time.
Main Results:
- DnoisE effectively detects and merges erroneous amplicons in coding DNA barcodes.
- The program leverages natural codon variability for improved denoising accuracy.
- Parallelizable nature of DnoisE significantly speeds up processing on computer clusters.
- DnoisE supports various input formats for seamless integration into existing pipelines.
Conclusions:
- DnoisE represents a significant advancement in DNA metabarcoding data processing for coding markers.
- The tool enhances the reliability of biodiversity assessments by mitigating sequencing errors.
- DnoisE offers a flexible and efficient solution for researchers utilizing coding DNA barcodes.
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