## Code All code used for polishing, masking and reannotation of the A. hypochondriacus reference genome. ### Order of usage: - code/genome_polishing/ polish the previously published A. hypochondriacus reference genome - code/repeat_masking/ to prepare computational annotation, softmask repetitive elements in the polished genome - code/braker2/ perform computational annotation of the softmasked reference genome using BRAKER2 - code/isoseq_assembly/ assembly long read transcript sequencing data and compare effects of genome polishing on reported completeness - code/merge_annotation/ merge computational annotation with long-read transcript sequencing data and process output into genome annotation v2.2 - code/annotation_analysis/ identify flavonoid and betalain pathway genes, as well as MYB transcription factors in the genome annotation v2.2 - code/other_inferences/ mapping of chloroplast and mitchondrium sequences to the reference genome, analysis of mapping coverage bias - code/BSA/ bulk segregant analysis and analysis of RNA-seq data from pooled flower tissue
Tom Winkler
authored