title: "Mytilus spp. ddRADseq (SphI-HF and MluCI, 50 bp trimmed to 35 bp), Sete, France": Sample "Sete, France"
design: "Restriction site-associated DNA libraries were prepared following the protocol of Peterson et al (2012) with slight modifications to account for the Mytilus spp. genome size and high polymorphism (Rodriquez-Juiz et al 1996, Cruz et al 2005, Saavedra et al 2006) using restriction enzymes SphI-HF and MluCI. Sixty individuals were pooled per library and sent to the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley for 50bp single-read Library Sequencing on the HiSeq2000 platform (Illumina, San Diego, CA, USA). \n We discarded Casava "filtered" flagged reads using the fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon /fastq_illumina_filter), and demultiplexed using the unique P1 barcodes with Sabre (https://github.com/najoshi/sabre). An additional 5 bp was trimmed from both the 5' and 3' end of each read, with the final read length standardized to 35 bp, and applied another quality filter (Phred score >20) with a custom Python wrapper and Sickle (https://github.com/najoshi/sickle). References: Cruz F, Perez M, Presa P (2005) Distribution and abundance of microsatellites in the genome of bivalves. Gene, 346, 241-247. \n Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS ONE, 7, e37135. \n Rodriquez-Juiz AM, Torrado M, Mendez J (1996) Genome-size variation in bivalve molluscs determined by flow cytometry. Marine Biology, 126, 489-497. \n Saavedra C, Bachere E (2006) Bivalve genomics. Aquaculture, 256, 1-14."