Fig. 2 | Scientific Data

Fig. 2

From: Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Fig. 2

Bioinformatic pipeline used to analyze mixed 16S and 18S rRNA amplicons generated from three-domain universal SSU rRNA primer set 515Y/926R from unfractionated seawater collected in the GRUMP collaboration. The unique features of this pipeline include an initial database-dependent in silico splitting step after PCR amplification and sequencing, parallel 16S rRNA and 18S rRNA denoising pipelines, and a correction-based merging step − allowing for the recovery of both 16S rRNA and 18S rRNA information in a single ASV table. Note that separate analysis pipelines are required due to the non-overlapping nature of forward and reverse 18S rRNA reads which would otherwise cause them to be discarded in bioinformatic pipelines that are dependent on read merging (as is common for most rRNA-based amplicon pipelines). The pipeline is based primarily in the QIIME2 framework and has been implemented and tested with Ubuntu-based Linux distributions.

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