18S rDNA miTags information for Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013)

ABSTRACT: 18S rRNA gene miTags (metagenomic Illumina tags, i.e., 18S rRNA gene assemblies derived from metagenomes sequenced with an Illumina platform) for sizes fractions >0.8 µm (0.8-5 µm, 0.8-2000 µm, 3-20 µm, 5-20 µm, 20-180 µm, 180-2000 µm). We extracted metagenomic reads for rRNA using SortMeRNA (Kopylova, Noé & Touzet 2012 Bioinformatics 28.24: 3211-3217) and those with ≥100 bp length with no Ns were dereplicated at the study level using VSEARCH v2.18 (Rognes et al. 2016 PeerJ 4:e2584). The resulting unique sequences were pairwise compared to PR2 v4.14 (Guillou at al. 2013 41.D1: D597-D604) using the VSEARCH's command --usearch_global to find the best hit defined as the reference sequence with the least differences in the region covering 100 percent of the query sequence. Only hits with ≥80% identity were kept. Each unique sequence inherits the taxonomy of the best hit and, in case of ties, the last common ancestor of the reference sequences is used. If you use this dataset please cite: Pierella Karlusich et al 2023 Molecular Ecology Resources (doi: 10.1111/1755-0998.13592)

ORGANISM(S): eukaryotes protists plankton

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PROVIDER: S-BSST762 | biostudies-other |

SECONDARY ACCESSION(S): PRJEB402

REPOSITORIES: biostudies-other