Cite:Structural variation and parallel evolution of apomixis in citrus during domestication and diversification
https://doi.org/10.1093/nsr/nwac114
see:https://doi.org/10.5281/zenodo.5748662
A groups of data and scripts in the analysis
Multi_test.py //perform multiple test
Specific_Species_marker_step1.py //prepare a specific species marker file, I divided it into three steps. Specific_Species_marker_step2.py Specific_Species_marker_step3.py
admixture_sorted_on_tree.py //sort the admixture results based on a phylogeny
deleterious_sites.txt //a file including deleterious sites
deletrious_stats.py // statistic the deleterious sites in each samples, there are three models as the paper
hemizygosity_stats.py //count the hemizygosity regions(genes) in the genome
reduce_ref_bias_on_outgroup.py //reduce the reference bias by outgroup variants
used_docker.list // a list including software in docker, I make a lot of docker imgaes which could be directly used, 3ks!! ):
Anno.SIFT.bed // a bed file used in SIFT statistics.
apomixis_transition.slim // a slim3 scripts for apomxixis transiton after admixture
BSA.pipeline //a pipeline for bulked segregant analysis(BSA) analysis
Dsuite.pipeline //a pipeline for Dsuite analysis
SV_detects.pipeline //a pipeline for SV_detect using delly and lumpy
popoTE2.pipeline //a pipeline for MITE insertion analysis
population_strcture.pipeline //a pipeline for population strcture analysis
smcpp.pipeline //a pipeline for effective population size anlysis