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benchmark_sets
benchmark_sets
 
 
Jaccard_distance_between_callsets.sh
Jaccard_distance_between_callsets.sh
 
 
LD_block.sh
LD_block.sh
 
 
Picky_SVIM_filter_for_supporting_reads.sh
Picky_SVIM_filter_for_supporting_reads.sh
 
 
README.md
README.md
 
 
SNP_calling_using_WGS_data.sh
SNP_calling_using_WGS_data.sh
 
 
SV_detection.sh
SV_detection.sh
 
 
Sim-it_config_HiFi
Sim-it_config_HiFi
 
 
Sim-it_config_ONT
Sim-it_config_ONT
 
 
adjust_SURVIVOR_merge_output.r
adjust_SURVIVOR_merge_output.r
 
 
benchmark_pipeline.sh
benchmark_pipeline.sh
 
 
detection_performance_evaluation.sh
detection_performance_evaluation.sh
 
 
mean_median_r2_LD_block.r
mean_median_r2_LD_block.r
 
 
reads_downsampling.sh
reads_downsampling.sh
 
 
sequencing_depth_coverage.sh
sequencing_depth_coverage.sh
 
 

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The key scripts relevant to structural variation (SV) detection in pigs are provided. The SV benchmark sets of five pig breeds compiled based on long reads from 3rd-generation sequencing platforms, i.e., Pacbio HiFi and ONT

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