Tara Mission Microplastics rDNA 18S V9 ASV table (DADA2)

Description

This repository contains the rDNA 18S V9 ASV table (DADA2) for Tara Mission Microplastics built with nf-core/ampliseq.

Files

tara-plastic_18s-v9_ampliseq_report.html: nf-core/ampliseq report detailing each bioinformatic step.

tara-plastic_18s-v9_context.tsv.gz: Contextual data table with 25 tab separated fields. For each sample, information such as the sampling protocol, temperature and nutrients concentration can be found.

tara-plastic_18s-v9_dada2_phyloseq.rds: ASV table in phyloseq format, see below for more details about the ASV table.

tara-plastic_18s-v9_dada2_table.tsv.gz: ASV table with 269 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (domain to species) with dada2's assignTaxonomy() using PR2 5.0.0. The per sample read numbers for each ASV (n=82,612) are indicated in the columns from I_LOIRE_S03_S325-T_PA to G_TIBRE_S01_CG_POM). Each sample name is composed as followed {RIVER_CODE}_{RIVER_NAME}_{STATION_NUMBER}_{PROTOCOL}_{SAMPLE_TYPE}.

ASV table assembly

The ASV table has been assembled with nf-core/ampliseq version 2.7.1. More details can be found in the ampliseq report (tara-plastic_18s-v9_ampliseq_report.html) and all the scripts are gathered in this gitlab repository