DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets

Author:

Antich Adrià1,Palacín Creu2,Turon Xavier1,Wangensteen Owen S.3

Affiliation:

1. Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB- CSIC), Blanes (Girona), Catalonia, Spain

2. Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia, Spain

3. Norwegian School of Fishery Science, UiT The Arctic University of Norway, Tromsø, Troms og Finnmark, Norway

Abstract

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.

Funder

PopCOmics

MARGECH

BigPark from the Spanish Government

UiT The Arctic University of Norway

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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