- Raw scripts/Pipeline for the "Jaltomata Genome" Project.
- detailed information for each step are recorded in the corresponding bash script
- Each bash script might combine scripts for multiple runs (need to check before running)
- Still in updating!
qsub masurca.sh
python genome_stat.py -i final_assembly.fasta -s 1500000000
qsub cegs_eval.sh
qsub mapping.sh
qsub blast_contaminants.sh
qsub organelle_assembly.sh
qsub repeat_annot2.sh
Genome annotation using the pipeline Maker (need to change maker_opts.ctl step by step; detail in bash script)
qsub maker.sh
qsub function_annotation.sh
qsub ortholog_inference.sh
qsub phylogeny_reconstruction.sh
qsub gene_family_analyses.sh
qsub go_enrichment.sh
qsub candidate_analyze.sh
qsub dnds_test.sh