Computational protocol: Mesozooplankton Graze on Cyanobacteria in the Amazon River Plume and Western Tropical North Atlantic

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Protocol publication

[…] Sequencing output was downloaded from the Torrent Server using Torrent Suite v3.0 to obtain the FastQ file. A total of 33 libraries were created using the barcoded sequences. Denoising was performed with Acacia () and the open-source bioinformatics program Mothur () was used to trim and align the sequences. Chimera sequences were removed using UCHIME and remaining sequences for each library were classified using the Greengenes database at confidence of greater than or equal to 0.80. Relative abundance of each taxa was calculated by dividing the number of classified sequences by total number of sequences in each library. All cyanobacteria sequences identified through Greengenes database were subsampled and subsequently reclassified through the SILVAngs pipeline with the SILVA 128 reference library (). Additionally, principal coordinate analysis (PCoA) was performed on square-root transformed relative abundance data in PRIMER 7 to identify patterns in microbial diversity between libraries. The raw sequence reads have been submitted to National Center for Biotechnology Information and are available under Bioproject number PRJNA387277. […]

Pipeline specifications

Software tools Acacia, mothur, UCHIME, SILVAngs
Databases Greengenes
Application 16S rRNA-seq analysis
Diseases Spinocerebellar Ataxias
Chemicals Carbon, Nitrogen