Helichrysum paper

Scripts and commands used to assemble and analyze Helichrysum genome

1. general_commands.sh is a shell file including all the commands run to do the assembly and annotate the genome. It is a guideline of the parameters used at each stage and the entire process is described in the Methods section of the paper.

2. annotation_pipeline.sh is a shell file with the functional annotation pipeline used to annotate the proteins taking as input a transcripts file and a list of protein databases to compare with. It was written to work in parallel in an LSF environment.

3. analyze_expression_of_candidate_enzymes.R is an R script that reads the RNAseq counts, the annotation files obtained in 1. and 2., and blastp searches with query candidate enzymes and finally creates and run a function for counts normalization and coexpression analysis using DEseq2 and CEMItool respectively. Besides the typical outputs of CEMItool, it outputs an excel file filtering the genes according to the candidate enzymes.

4. circlize_plot.R is an R script that reads the density of genes, the density of TEs, the coverage of the RNAseq, and the genomic position of candidate genes and makes a circos plot with circlize package.

5. metabolic_gene_cluster.R is an R script that takes the structural and functional annotation and plots the genes present in the selected genomic coordinates using the gggenes package.