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

• Published in: PeerJ
• Main Authors: Antich, Adrià, Palacín, Cruz, Turon, Xavier, Wangensteen, Owen S.
• Format: Article in Journal/Newspaper
• Language: English
• Published: PeerJ 2022
• Subjects: Metabarcoding; Bioinformatic pipelines; Metaphylogeography; Entropy correction; Denoising algorithms; Coding markers; Arctic; Norway; Arctic University of Norway; UiT The Arctic University of Norway
• Online Access: http://hdl.handle.net/10261/258251

Este artículo contiene 16 páginas, 5 figuras. 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. This research was funded by the projects PopCOmics (CTM2017-88080, MCIN/AEI/10.13039/ 501100011033 and ``ERDF A way of making Europe'', EU), MARGECH (PID2020- 118550RB, MCIN/AEI/10.13039/501100011033), and BigPark (OAPN, 2462/2017) from the Spanish Government. The publication charges for this article have been funded by a grant from the publication fund of UiT The Arctic University of Norway. Peer reviewed