LOP allele sequence generated from the MaSuRCA genome assembly of PH70 Pilosella piloselloides var praealta

<p>This contains three documents. The first is the clean sequence of the LOP allele sequence generated from the MaSuRCA genome assembly that was used in the Msc thesis: An Investigation into the Genetic Forces Shaping the LOP Locus of Pilosella Piloselloides var praealta.</p> <p>The second and third are the annotated version of this reference.</p> <p>One annotated LOP reference sequence is annotated with:</p> <ol> <li>Gene annotation generated using BRAKER</li> <li>Transposon annotation generated using EDTA</li> <li>RNA-seq data aligned to the LOP allele sequence</li> <li>EMS mutant variants generated from the GatK variant calling pipeline</li> </ol> <p>The second annotated LOP reference is annotated with:</p> <ol> <li>Gene annotation generated using BRAKER</li> <li>Transposon annotation generated using EDTA</li> <li>Transcriptome (Trinity assembly) aligned to the LOP allele sequence</li> <li>EMS mutant variants generated from the GatK variant calling pipeline</li> </ol><p></p>