Update README.md

tli14 · Aug 21, 2022 · 965db8b · 965db8b
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@@ -18,57 +18,62 @@ This repository provides codes and files to reproduce data and figures from the
 ## Scripts
 * **Python_Shell_scripts**
   - **Genome_Data_Collection: collect and analyze genome data.**
-    - [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.<br> 
+    - [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.<br> 
 
   - **17_species: pan-genome analysis for 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.<br> 
+    - [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.<br> 
 
   - **MAG_Simulation: simulate MAGs from complete genomes.**
-    - [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. 
-    - [generate_numbers.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/generate_numbers.sh): Generate numbers for genome list to assign random fragmentation/incompleteness/contamination numbers.
-    - [simulation.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/simulation.sh): Automatic simulation scripts.
-    - [batch_files.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/batch_files.sh): Batch files for simulation.
-    - [multiple_dataset.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/multiple_dataset.sh): Generate multiple datasets for testing the dataset variations.<br> 
+    - [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. 
+    - [generate_numbers.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/generate_numbers.sh): generate numbers for genome list to assign random fragmentation/incompleteness/contamination numbers.
+    - [simulation.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/simulation.sh): automatic simulation scripts.
+    - [batch_files.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/batch_files.sh): batch files for simulation.
+    - [multiple_dataset.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/3.MAG_Simulation/multiple_dataset.sh): generate multiple datasets for testing the dataset variations.<br> 
 
-  - **Mixed_datasets: generate mxied datasets contain MAGs and complete genomes.**
-    - [rad_combine.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/rad_combine.sh): Generate mixed datasets with different percentage of MAGs.
-    - [copy_ori_file.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/copy_ori_file.py): Generate mixed datasets by combining original and simulated MAG dataset.
-    - [Pan-genome_and_summary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/Pan-genome_and_summary.sh): Perform pan-genome analysis for mixed datasets.
-    - [loop_rad_combine.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/loop_rad_combine.sh): Run rad_combine.sh for multiple times.
-    - [roary_sum.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/roary_sum.py): Summary Roary results for multiple mixed datasets.<br> 
+  - **Mixed_datasets: generate and analyze mxied datasets contain MAGs and complete genomes.**
+    - [rad_combine.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/rad_combine.sh): generate mixed datasets with different percentage of MAGs.
+    - [copy_ori_file.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/copy_ori_file.py): generate mixed datasets by combining original and simulated MAG dataset.
+    - [Pan-genome_and_summary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/Pan-genome_and_summary.sh): perform pan-genome analysis for mixed datasets.
+    - [loop_rad_combine.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/loop_rad_combine.sh): run rad_combine.sh for multiple times.
+    - [roary_sum.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/4.Mixed_datasets/roary_sum.py): summary Roary results for multiple mixed datasets.<br> 
 
-  - **Three_tools: pan-genome analysis using three different tools.**
+  - **Three_tools: perform pan-genome analysis using three different tools.**
     - **[Anvi'o](https://github.com/tli14/PanMAGs/tree/main/Python_Shell_scripts/5.Three_tools/Anvi'o):**
-      - [Anvi'o.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Anvi'o/Anvi'o.sh): Use Anvi'o for pan-genome analysis.
-      - [genbank-parser.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Anvi'o/genbank-parser.py): To generate a tab-delimited file to define external gene calls from Genbank files given by Prokka.
+      - [Anvi'o.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Anvi'o/Anvi'o.sh): use Anvi'o for pan-genome analysis.
+      - [genbank-parser.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Anvi'o/genbank-parser.py): generate a tab-delimited file to define external gene calls from Genbank files given by Prokka.
     - **[BPGA](https://github.com/tli14/PanMAGs/tree/main/Python_Shell_scripts/5.Three_tools/BPGA):**
-      - [gen_faa.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/BPGA/gen_faa.sh): Rename the .faa files.
-      - [sort_faa.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/BPGA/sort_faa.sh): Prepare .faa files for BPGA pan-genome analysis.
+      - [gen_faa.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/BPGA/gen_faa.sh): rename the .faa files.
+      - [sort_faa.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/BPGA/sort_faa.sh): prepare .faa files for BPGA pan-genome analysis.
       - [summary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/BPGA/summary.sh): BPGA pan-genome result summary.
     - **[Roary](https://github.com/tli14/PanMAGs/tree/main/Python_Shell_scripts/5.Three_tools/Roary):**
-      - [gen_gff.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/gen_gff.sh): Rename the .gff files.
-      - [prokka_generate.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/prokka_generate.sh): Generate prokka annotation script.
-      - [bash_prokka.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/bash_prokka.sh): PROKKA annotation.
-      - [roary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/roary.sh): Generate Roary pan-genome analysis script.
-      - [sbatch_roary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/sbatch_roary.sh): Run Roary analysis.
-      - [rad_roary_sum.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/rad_roary_sum.py): Summarize roary results.<br>
-
-  - **COG_analysis: The Clusters of Orthologous Genes (COG) analysis.**
-    - [prepare_files.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/prepare_files.sh): Prepare for COG functional analysis for core gene families after pan-genome analysis.
-    - [rpsblast_batch.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rpsblast_batch.sh): Use rps-blast to perform domian search and then determine COG categories.
-    - [rps_select.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rps_select.py): Select non-overlap domains for each genes.
-    - [rps2COG.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rps2COG.py): Extract COG information from rpsblast results after the selection of non-overlap domains.
-    - [core_rps.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/core_rps.sh): Run rps-blast.
-    - [rpsblast_to_COG.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rpsblast_to_COG.sh): Select non-overlap domains for rps-blast results and assign the COG categories.<br>
+      - [gen_gff.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/gen_gff.sh): rename the .gff files.
+      - [prokka_generate.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/prokka_generate.sh): generate prokka annotation script.
+      - [bash_prokka.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/bash_prokka.sh): prokka annotation.
+      - [roary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/roary.sh): generate Roary pan-genome analysis script.
+      - [sbatch_roary.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/sbatch_roary.sh): run Roary analysis.
+      - [rad_roary_sum.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/5.Three_tools/Roary/rad_roary_sum.py): summarize roary results.<br>
 
+  - **COG_analysis: perform the clusters of orthologous Genes (COG) analysis.**
+    - [prepare_files.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/prepare_files.sh): prepare for COG functional analysis for core gene families after pan-genome analysis.
+    - [rpsblast_batch.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rpsblast_batch.sh): use rps-blast to perform domian search and then determine COG categories.
+    - [rps_select.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rps_select.py): select non-overlap domains for each genes.
+    - [rps2COG.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rps2COG.py): extract COG information from rpsblast results after the selection of non-overlap domains.
+    - [core_rps.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/core_rps.sh): run rps-blast.
+    - [rpsblast_to_COG.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/6.COG_analysis/rpsblast_to_COG.sh): select non-overlap domains for rps-blast results and assign the COG categories.<br>
 
+  - **Core_gene: extract and analyze core genes.**
+    - **[Anvi'o](https://github.com/tli14/PanMAGs/tree/main/Python_Shell_scripts/7.Core_gene/Anvi'o):**
+      - [Anvio_extract_core.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/7.Core_gene/Anvi'o/Anvio_extract_core.sh): extract core genes from anvi'o outputs.
+      - [extract_all_fasta_seq.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/7.Core_gene/Anvi'o/extract_all_fasta_seq.py): extract all gene sequences in gene clusters.
+      - [Anvio_extract_ref_core_seq.py](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/7.Core_gene/Anvi'o/Anvio_extract_ref_core_seq.py): Select the longest core sequence from each gene cluster as the core representative sequence.
+      - [blast_generate.sh](https://github.com/tli14/PanMAGs/blob/main/Python_Shell_scripts/7.Core_gene/Anvi'o/blast_generate.sh):