RAD capture sequencing of Procambarus clarkii
We extracted genomic DNA either using a DNeasy Blood & Tissue Kit (Qiagen) or a bead-based protocol in 96-well plates, following methods in Ali et al. (2016). RAD capture libraries were prepared using the BestRAD protocol (Ali et al. 2016). Genomic DNA was digested with the SbfI restriction enzyme. Capture reactions were carried out with custom baits (Ref#201001-90, Arbor Biosciences) using the MyBaits Version 4.01 protocol. Paired-end 150bp Illumina sequencing was conducted across two lanes at the Research Technology Support Facility (RTSF) Genomics Core at Michigan State University. One lane was sequenced in 2021 the other in 2022. The forward and reverse files for each raw sequence library were exchanged whenever the barcode was found at the start of read two using a previously published perl script (bRAD_flip_trim.pl). Libraries were demultiplexed using process_radtags in Stacks v. 2.786