Nanopore sequencing of Wolbachia endosymbiont of Rhagoletis cingulata wCin3: Wolbachia reads for SV scans
An ONT LSK109 ligation library was prepared from HMW DNA from a single Rhagoletis fly and sequenced on a R9.4.1 MinION flowcell at low coverage. Raw data was basecalled using the Guppy v6.01 with the SUP model and quality filtered (>Q8 and >500 bp). Reads were mapped to the assembled Wolbachia genome with minimap2 and unmapped reads were dropped with Samtools. Reads were used for structural variant scans.