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2 changes: 1 addition & 1 deletion 1_Detection/README.md
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Expand Up @@ -24,7 +24,7 @@ All scripts are implemented in MATLAB. The order of the scripts indicates the or
[**A0_VariantFiltering.m**](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A0_VariantFiltering.m) and is run on the donor sequencing reads aligned to the recipient used for the hybrid organisms. It is expected to be run with the same filter paramters as used for the variant filtering of the hybrid strains. It gives a special masterlist **.mat** output that can be used for the [**A1_SNP2CNP.m** ](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A1_SNP2CNP.m) script.

[**A0c_AccessoryGenome.m**](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A0c_AccessoryGenome.m)
- Here, we detect the accessory genome parts of the recipient reference with respect to the donr (or vice versa). The accessory regions found here are excluded from the replacement detection performed with [**A1_SNP2CNP.m** ](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A1_SNP2CNP.m). As an input, this script takes the **.vcf** output from the **mpileup** function run in [2_CombiScriptSamtools.sh](https://github.com/Easybel/DetectionGV/blob/main/0_WGSPipeline/2_CombiScriptSamtools.sh). For all positions that have a read depth below the threshold set in [**A0_VariantFiltering.m**](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A0_VariantFiltering.m), the script identifies consecutive regions longer than 150 bp. These are collected as accessory regions.
- Here, we detect the accessory genome parts of the recipient reference with respect to the donor (or vice versa). The accessory regions found here are excluded from the replacement detection performed with [**A1_SNP2CNP.m** ](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A1_SNP2CNP.m). As an input, this script takes the **.vcf** output from the **mpileup** function run in [2_CombiScriptSamtools.sh](https://github.com/Easybel/DetectionGV/blob/main/0_WGSPipeline/2_CombiScriptSamtools.sh). For all positions that have a read depth below the threshold set in [**A0_VariantFiltering.m**](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A0_VariantFiltering.m), the script identifies consecutive regions longer than 150 bp. These are collected as accessory regions.

[**A0d_Multimapper.m**](https://github.com/Easybel/DetectionGV/blob/main/1_Detection/A0d_Multimapper.m)
- Prior to using this script, the genome **fasta** of the genome reference is blasted to itself and the hit table is obtained.
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