RD-Analyzer

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RD-Analyzer
===
_In silico_ region of difference (RD) analysis of _Mycobacterium tuberculosis_ complex from sequence reads

Files
---
**RD-Analyzer.py:** the standard RD-Analyzer used for deletion prediction of previously defined RD markers and strain identification of _Mycobacterium tuberculosis_ complex based on these markers.  
**RD-Analyzer-extended.py:** the extended RD-Analyzer used for deletion prediction of user-specified RD sequences.  
**Reference/RDs30.fasta:** sequences of previously defined RD markers used in the standard RD-Analyzer.  
**Reference/Lineage4.fasta:** sequences of potential Lineage 4 markers identified in the manuscript.

Prerequisites
---
Python 2.7  
BWA-MEM  
SAMtools (v 0.1.19)

Standard RD-Analyzer
---
**Usage:**
```shell
python2.7 RD-Analyzer.py [options] FASTQ_1 FASTQ_2(optional)
```

**Options:**
```
  --version          show program version number and exit
  -h, --help         show this help message and exit
  -d, --debug        enable debug mode, keeping all intermediate files

-O OUTDIR, --outdir=OUTDIR
        output directory [Default: running directory]
  -o OUTPUT, --output=OUTPUT
        basename of output files [Default: RD-Analyzer]
 
  -p, --personalized
        use personalized cut-offs
  -m MIN, --min=MIN
        read depth cut-off (in the unit of average depth, 0-1), used when '-p' is set
  -c COVERAGE, --coverage=COVERAGE
        sequence coverage cut-off (0-1), used when '-p' is set
```

**Suggestions:**
Users are suggested to use the default cut-offs which are optimized by us.

Extended RD-Analyzer
---
**Usage:**
```
python2.7 RD-Analyzer-extended.py [options] REF.FASTA FASTQ_1 FASTQ_2(optional)
```

**Options:**
```
  --version          show program version number and exit
  -h, --help         show this help message and exit
  -d, --debug        enable debug mode, keeping all intermediate files

-O OUTDIR, --outdir=OUTDIR
        output directory [Default: running directory]
  -o OUTPUT, --output=OUTPUT
        basename of output files [Default: RD-Analyzer]
```

**Input files:**  
REF.FASTA - Reference sequences used should be in a fasta file with the header lines prepared as below:  
* Four fields are reuiqred in the header line, which should be separated with '-'.
* Field one: reference sequence name
* Filed two: read-depth cutoff to be used (in the unit of average depth, in a 0-1 scale). Specify 'default' if want to use default parameters (0.09)
* Field three:  sequence coverage cut-off (in a 0-1 scale). Specify 'default' if want to use default parameters (0.5)
* FIled four: descriptive information of the RD to be shown if the RD is detected.
* An example header line: **>Lineage4.6.1.2/1-default-default-Lineage4.6.1.2/1**
* **Notice:** 1. Don't include space in the header file. 2. Don't use '-' unless as filed deliminator

RD-Analyzer

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