NaMeco - metataxonomic tool for 16S Nanopore long reads clustering and annotation

Due to the length of the output reads and availability, complete 16S rRNA gene nanopore sequencing offers great potential for metataxonomic studies. However, a relatively high error rate poses a significant challenge for bioinformatic processing, often concealing the abovementioned advantages. As a result, despite the length of obtained reads, taxonomy annotations often could not be resolved higher than the genus level. Additionally, the choice of the taxonomic database may significantly affect the final output. In this work, we introduce a new tool, NaMeco, designed to handle long 16S rRNA reads sequenced by Oxford Nanopore Technologies with minimum effort from the user side. Our tool performs read clustering and taxonomic annotation of resulted clusters, providing as the output cluster counts table, taxonomic annotations of clusters, representative sequences in fasta format and taxa counts at each taxonomy rank. Output files are compatible with the Qiime2 pipeline and can be imported into the required format for downstream analyses. We also demonstrated that NaMeco, in combination with the GTDB database, outperforms such tools as NanoCLUST, EPI2ME and Kraken2, providing higher taxonomy accuracy and detection rates.