Update README.md

README.md

@@ -16,8 +16,21 @@ This repository provides codes and files to reproduce data and figures from the
 * Information about R packages needed to run R codes can be found in [R_packages](https://github.com/tli14/PanMAGs/blob/main/R_packages).
 
 ## Scripts
-* Python_Shell_scripts
-  - 1.Genome_Data_Collection:
+* **Python_Shell_scripts**
+  - 1. Genome_Data_Collection:
     - [download_all_complete_genome_fasta.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/1.Genome_Data_Collection/download_all_complete_genome_fasta.sh): Download complete bacteria genomes from assembly_summary.txt.
     - [download_genus_contaminaton_genomes.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/1.Genome_Data_Collection/download_genus_contaminaton_genomes.sh): Download bacteria genomes as contamination datasets.
     - [fastANI.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/1.Genome_Data_Collection/fastANI.sh): Calculate average nucleotide identity (ANI) for bacteria species.
+ - 2. 17_species:
+    - [prokka.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/2.17_species/prokka.sh): Genome annotation by using Prokka.
+    - [gen_gff.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/2.17_species/gen_gff.sh): Rename .gff files from Prokka results.
+    - [roary_species.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/2.17_species/roary_species.sh): Pan-genome analysis by using Roary.
+    - [sbatch_roary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/2.17_species/sbatch_roary.sh): Run multiple jobs for pan-genome analysis.
+- 3. MAG_Simulation:
+    - [fragmentation.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/fragmentation.py): Fragmentation simulation - random cut the genome to fragments (random number of fragments).
+    - [fragmentation_avrg_length.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/fragmentation_avrg_length.py): Fragmentation simulation - random cut the genome to fragments (random length of fragments).
+    - [incompleteness.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/incompleteness.py): Incompleteness simulation - remove a percentage of sequence length from each fragment.
+    - [contamination.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/contamination.py): Contamination simulation - add fragments from other genomes in the same species (intraspecies).
+    - [contamination_genus.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/contamination_genus.py): Contamination simulation - add fragments from other genomes in the same genus (interspecies).
+    - [random_distribution](https://github.com/tli14/PanMAGs/tree/main/Python_Shell_scripts/3.MAG_Simulation/random_distribution): 
+Generate random numbers following F distribution for simualtion.