Sequence quality determination and filtering of RADtags
The DNA from individual fish was digested with Eco RI and
paired-end sequencing libraries with an insert size of 200–400 bp were
constructed. These RAD libraries were subsequently sequenced using the
Illumina HiSeq PE150 platform.
The raw sequence data were filtered by removal of reads with
low-quality, reads with adapter contamination, reads with ≥ 10%
unidentified nucleotides (N), and reads for which ≥ 50% of the length
had a phred quality ≤ 5.