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

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.

The second and third are the annotated version of this reference.

One annotated LOP reference sequence is annotated with:

Gene annotation generated using BRAKER
Transposon annotation generated using EDTA
RNA-seq data aligned to the LOP allele sequence
EMS mutant variants generated from the GatK variant calling pipeline

The second annotated LOP reference is annotated with:

Gene annotation generated using BRAKER
Transposon annotation generated using EDTA
Transcriptome (Trinity assembly) aligned to the LOP allele sequence
EMS mutant variants generated from the GatK variant calling pipeline