Merge branch 'main' of github.com:zy-optimistic/GAEP into main

README.md

@@ -15,13 +15,13 @@ cd GAEP
 ```
 gaep <command> [options]
 
-pipe        let GAEP to determine the module to be executed based on the input data   
-stat        report genome basic information  
-macc        base accuracy based on reads mapping  
-kacc        base accuracy based on K-mer  
-bkp         misassembly breakpoints detected  
-snvcov      SNV-coverage dot plot  
-busco       run busco v5  
+pipe   (NGS,TGS,trans)  let GAEP to determine the module to be executed based on the input data   
+stat                    report genome basic information  
+macc   (NGS)            base accuracy based on reads mapping  
+kacc   (NGS)            base accuracy based on K-mer  
+bkp    (TGS)            misassembly breakpoints detected  
+snvcov (NGS,TGS)        SNV-coverage dot plot  
+busco                   run busco v5  
 ```
 
 ## Running example

test/simulate/README.md

@@ -3,6 +3,11 @@ These scripts are used to simulate the misassemblies using a template genome.
 
 # Running
 ```bash
+#At first, we recommend to remove the contigs less than 500k in template.fasta and split the template.fasta from Ns.
+
+#Index
+samtools faidx template.fasta
+
 #Randomly generate the positions of misassemlies
 perl simu_misassembly_posi.pl template.fasta > position.txt
 
@@ -11,4 +16,26 @@ sort -k1V -k2n position.txt | perl move_redundant.pl > position_redun.txt
 
 #Introduce misassemblies by positions. Two FASTA files will be output: one for the reference and one for simulation.
 perl simu_misassembly.pl template.fasta
+
+mv *ref.fasta template.ref.fasta
+mv *simu.fasta template_simu.fasta
+
+#PacBio reads simulation
+pbsim template.ref.fasta --prefix simu_pb --depth 50 --length-min 5000 --length-max 50000 --hmm_model XXX/P6C4.model --length-mean 20000
+
+#The template_simu.fasta is the final assembly with simulated misassemblies, and the template.ref.fasta is the reference.
+```
+
+# Output 
+The positions of simulated misassemblies can be found in STDOUT.
+```
+#Format:
+No  strand  contig  type  length  start  end
+41	1	chr1	ins	48762	14640630	14640631
+41	2	chr1	ins	48762	14697478	14746240
+
+#For strand:
+#1: Misassemblies corresponding to positions in the reference sequence.
+#2: Misassembly positions in the simulated sequence.
 ```
+Typically, retaining only the rows with a strand value of 2 will provide the positional information of the final simulated misassemblies.