Study of the SKUD affecting the sea cucumber Holothuria scabra in Madagascar (metagenomic shotgun analyses)

Four H. scabra integument samples were analysed:(i) ulcerated integument, individual 1/replicate 1 (1RU)(ii) ulcerated integument, individual 2/replicate 2 (2RU)(iii) healthy integument, individual 1/replicate 1 (1RS)(iv) healthy integument, individual 2/replicate 2 (2RS)Shotgun metagenome libraries were prepared and sequenced on Illumina NovaSeq 6000 platform (2x150 bp) at Eurofins Genomics (www.eurofinsgenomics.eu). Raw data were uploaded as FASTQ after demultiplexing of paired-end reads. Quality processing (i.e. dynamic trimming: minimum quality = 15, maximum low-quality basepairs = 5; detection and removal of adapter sequences using Skewer with default parameters 26) and deduplication was performed using MG-RAST 4.0.3 pipeline analysis.