The dataset contains 16 gzipped FASTQ files containing raw (multiplexed) Illumina sequencing data from hawksbill turtles. The two original library files were each split into 8 sub-files using the split command (BASH). To merge the sub-files into their respective libraries, run the following BASH commands (you will need Mac OSX or Linux): zcat eimbricata_ddrad_raw_seqs_1.fastq.part0* > eimbricata_ddrad_raw_seqs_1.fastq zcat eimbricata_ddrad_raw_seqs_2.fastq.part0* > eimbricata_ddrad_raw_seqs_2.fastq I highly recommend to compress (gzip ) the files after merging, since the uncompressed sizes are ~160gb per file. I haven't tested it, but it should be possible to simply proceed to cleaning, decloning and demultiplexing steps using just the 16 sub-files. Please see the methods listed in the manuscript and the supplementary information for details on how to process and analyze the raw data.