01_gap_close_polish.sh
02_repeat_masking.sh
03_synteny.sh
04_short_RNA_QC.sh
05_gene_prediction.sh
06_functional_annotation.sh
07a_SNP_UpSet.R
07b_select_high_dens_SNPs.R
07c_circos_SNPs.sh
07d_piecharts_SNPs.R
08a_transcription.sh
08b_clustering_TPM.R
08c_cluster_KEGG_enrichment.R
08d_ballgown_MF_DE.R