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.