PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

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BackgroundThe study of sample taxonomic composition has evolved from direct observations and labor-intensive morphological studies to different DNA sequencing methodologies.Most of these studies leverage the metabarcoding approach, which involves the amplification of a small taxonomically-informative portion of the genome and its subsequent high-throughput sequencing.Recent advances in sequencing technology brought by Oxford Nanopore Technologies have revolutionized the field, enabling portability, affordable cost and long-read sequencing, therefore leading to a significant increase in taxonomic resolution.However, Nanopore sequencing data exhibit a particular profile, with a higher error rate compared with Illumina sequencing, and existing bioinformatics pipelines for the analysis of such data are scarce and often insufficient, requiring specialized tools to accurately process long-read sequences.ResultsWe present PRONAME (PROcessing NAnopore MEtabarcoding data), an open-source, user-friendly pipeline optimized for processing anodized pearl price xbox raw Nanopore sequencing data.

PRONAME includes precompiled databases for complete 16S sequences (Silva138 and Greengenes2) and a newly developed and curated database dedicated to bacterial 16S-ITS-23S operon sequences.The user can also provide a custom database if desired, therefore enabling the analysis of metabarcoding data for any domain of life.The pipeline significantly improves sequence accuracy, implementing innovative error-correction strategies and taking advantage of the new sequencing chemistry to produce high-quality duplex reads.Evaluations using a mock community have shown that PRONAME delivers consensus sequences demonstrating at least 99.5% accuracy with standard settings (and up to 99.

7%), making it a robust tool for genomic analysis of complex verona wig multi-species communities.ConclusionPRONAME meets the challenges of long-read Nanopore data processing, offering greater accuracy and versatility than existing pipelines.By integrating Nanopore-specific quality filtering, clustering and error correction, PRONAME produces high-precision consensus sequences.This brings the accuracy of Nanopore sequencing close to that of Illumina sequencing, while taking advantage of the benefits of long-read technologies.