Update README.md

README.md

@@ -19,3 +19,36 @@ cd NGSNGS; make
 
 **NOTE:** Newer version of htslib which includes bam_set1 is required
 
+
+## GENERAL
+Next Generation Simulator for Next Generator Sequencing Data version 0.9.2.1 
+
+~~~~bash
+Next Generation Simulator for Next Generator Sequencing Data version 0.9.2.1
+
+Usage
+./ngsBriggs -bam -tab -ref -bed -len -chr -ibam -iref -ibed -ichr -obam -otab -oinf -olen -model -eps -isrecal -olik -nthreads
+	-> -bam: The bam file for inference;
+	-> -tab: The table file for inference;
+	-> -ref: The reference file for inference;
+	-> -bed: The bed file (1-based) for inference;
+	-> -len: The length mass probability distribution file for inference;
+	-> -chr: The focal chromosome for inference;
+	-> -ibam: The bam file for ancient strand fishing;
+	-> -iref: The reference file for ancient strand fishing;
+	-> -ibed: The bed file (1-based) for ancient strand fishing;
+	-> -ichr: The focal chromosome for ancient strand fishing;
+	-> -obam: The output bam file name;
+	-> -otab: The output table file name;
+	-> -oinf: The output inferred parameters file name;
+	-> -olen: The output length mass probability distribution file name;
+	-> -model: Specifying the model, either b (the biotin model) or nb (the non-biotin model);
+	-> -eps: The overall modern contamination rate, the value should be within the interval [0,1);
+	-> -isrecal: Choose 1 if recalibration based on length is needed, otherwise 0 (default);
+	-> -olik: The output nucleotide likelihood file;
+	-> -nthreads: Choose the number of threads to speed up the recalibration process.
+
+Example
+./ngsbriggs -bam /projects/korneliussen/people/wql443/NGSNGS/HgSimTest1.bam -ref /projects/korneliussen/people/wql443/NGSNGS/Test_Examples/Mycobacterium_leprae.fa.gz -model b
+
+~~~~