Sequences and scripts

# sequence-data folder The sequence-data folder contains all the metabarcoding data for this study and is organised in numbered folders. There is also a scripts folder here that contains the scripts used to generate the files in each step of the bioinformatics pipeline. See below a list of the sub-folders and a description of their contents... 1_raw (raw sequence data received from AGRF) 2_demux (demultiplexed files) 2_demux_trimmed (demultiplexed & trimmed reads) 3_merged (merged reads) 4_trimmomatic (quality filered reads) 5_trimmed (trimmed reads) 6_concat_not_unique (concantenated files) 7_concat_unique (concatenated files with duplicates removed) 8_derep (dereplicated reads) 9_denoised (reads following denoising steps) 10_length_filtered (reads post filtering by length) 11_chimeras_removed (chimeras removed) 12_mapped (tables resulting in the pipeline for use in taxonomic identification) 13_swarm (clustered reads into OTUs using swarm) 14_blast (echinoderm reads blasted against NCBI) 14_midori (all reads validated against MIDORI CO1 database) # community-data folder The community-data folder contains all the final files that were created at the end of the bioinformatics pipeline. The files were further curated and filtered in R and formatted for downstream analyses and figures.