Trypanosoma melophagium isolate:St. Kilda Genome sequencing and assembly

To identify the genomic basis of host and vector specificity in non-pathogenic trypanosomatids, T. melophagium was isolated from sheep blood collected on the island of St Kilda, Scotland. DNA was extracted from cultured cells using a MagAttract high molecular weight DNA Kit, following the manufacturer instructions, Qiagen, and cleaned via ethanol precipitation. The DNA was sequenced with the Oxford Nanopore Technology, ONT, MinION, following the Nanopore Rapid Sequencing protocol. Base-calling was performed in high accuracy mode using Guppy. The same DNA was sequenced with BGI DNBseq, 150bp reads. RNA was extracted with the RNeasy mini kit, Qiagen, including a DNAse step, following the manufactures instructions, and sequenced with BGIs DNBseq, 100bp reads. The submitted reads are untrimmed. Nanopore long reads were assembled using Wtdbg2. For the remainder of the polishing steps, BWA MEM was used to align short reads and Minimap2 was used to align ONT reads. ONT reads were aligned to the Wtdbg2 draft assembly and three iterations of Racon followed by one round of Medaka were performed. DNBseq reads were mapped to the Medaka polished assembly, and two iterations of Racon were performed. Short and long reads were aligned to the Racon polished assembly to complete two final iterations of polishing with Pilon. At each stage of polishing, the draft genome was assessed with BUSCO.