Similar protocols

Protocol publication

[…] se.inra.fr/galaxy/) was used for data processing []. In brief, paired reads were merged using FLASH []. After denoising and primer/adapters removal with cutadapt [], de novo clustering was done using SWARM that uses a local clustering threshold [], with aggregation distance d = 3 after denoising. Chimera were removed using VSEARCH []. We filtered the dataset for singletons and performed affiliation using Blast+ against the Silva database (release 128, September 2016) for 16S rRNA gene amplicons. For ITS2 metabarcoding, the Symbiodinium clade was assessed using blastn best hit against the nr/nt database of the NCBI []. To confirm blast identification, we performed phylogenetic analysis using MAFFT to produce sequence alignment and FastTree (GTR + CAT model) to compute tree with the approximately maximum-likelihood method. Finally, OTU tables were produced in a standard BIOM format for subsequent analyses., All statistical analyses were done using R version 3.3.1 ([], http://www.R-project.org). We used the phyloseq R package for community composition analysis [] to infer alpha diversity metrics at the OTU level, as well as beta diversity (between sample distance) from the OTU table. Community similarity was assessed by principal coordinate analysis (PCoA) using the Bray-Curtis dissimilarity index., We performed non-parametric Kruskal-Wallis tests (since normality of residuals and homogeneity of variances were rejected (Shapiro and Bartlett test, respectively)) to compare alpha diversity metrics (Chao1 and Shannon). When Kruskal-Wallis tests were significant, we then computed pairwise comparisons between group levels (post hoc analyses) with Bonferroni corrections for multiple testing using Dun […]

Pipeline specifications

Software tools MAFFT, FastTree, phyloseq