diff --git a/README.md b/README.md index d000f68..1ba3d72 100644 --- a/README.md +++ b/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 + +~~~~