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Fonio_smcpp.docx
Fonio_smcpp.docx
 
 
README.md
README.md
 
 
crea_smcpp_fonio_cult_Sample1.NEW.sh
crea_smcpp_fonio_cult_Sample1.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample10.NEW.sh
crea_smcpp_fonio_cult_Sample10.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample2.NEW.sh
crea_smcpp_fonio_cult_Sample2.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample3.NEW.sh
crea_smcpp_fonio_cult_Sample3.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample4.NEW.sh
crea_smcpp_fonio_cult_Sample4.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample5.NEW.sh
crea_smcpp_fonio_cult_Sample5.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample6.NEW.sh
crea_smcpp_fonio_cult_Sample6.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample7.NEW.sh
crea_smcpp_fonio_cult_Sample7.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample8.NEW.sh
crea_smcpp_fonio_cult_Sample8.NEW.sh
 
 
crea_smcpp_fonio_cult_Sample9.NEW.sh
crea_smcpp_fonio_cult_Sample9.NEW.sh
 
 
crea_smcpp_fonio_cult_group1.NEW.sh
crea_smcpp_fonio_cult_group1.NEW.sh
 
 
crea_smcpp_fonio_cult_group2.NEW.sh
crea_smcpp_fonio_cult_group2.NEW.sh
 
 
crea_smcpp_fonio_cult_group3.NEW.sh
crea_smcpp_fonio_cult_group3.NEW.sh
 
 
crea_smcpp_fonio_cult_group4.NEW.sh
crea_smcpp_fonio_cult_group4.NEW.sh
 
 
crea_smcpp_fonio_cult_group5.NEW.sh
crea_smcpp_fonio_cult_group5.NEW.sh
 
 
crea_smcpp_fonio_cult_group6.NEW.sh
crea_smcpp_fonio_cult_group6.NEW.sh
 
 
crea_smcpp_fonio_wild.NEW.sh
crea_smcpp_fonio_wild.NEW.sh
 
 
list_fonio_cultivated_Sample1.csv
list_fonio_cultivated_Sample1.csv
 
 
list_fonio_cultivated_Sample10.csv
list_fonio_cultivated_Sample10.csv
 
 
list_fonio_cultivated_Sample2.csv
list_fonio_cultivated_Sample2.csv
 
 
list_fonio_cultivated_Sample3.csv
list_fonio_cultivated_Sample3.csv
 
 
list_fonio_cultivated_Sample4.csv
list_fonio_cultivated_Sample4.csv
 
 
list_fonio_cultivated_Sample5.csv
list_fonio_cultivated_Sample5.csv
 
 
list_fonio_cultivated_Sample6.csv
list_fonio_cultivated_Sample6.csv
 
 
list_fonio_cultivated_Sample7.csv
list_fonio_cultivated_Sample7.csv
 
 
list_fonio_cultivated_Sample8.csv
list_fonio_cultivated_Sample8.csv
 
 
list_fonio_cultivated_Sample9.csv
list_fonio_cultivated_Sample9.csv
 
 
list_fonio_wildG1.csv
list_fonio_wildG1.csv
 
 
run_bamCaller_multipleChr_fonio.bash
run_bamCaller_multipleChr_fonio.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group1.bash
run_slurm_smcpp_fonio_cultivated_cv_Group1.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group2.bash
run_slurm_smcpp_fonio_cultivated_cv_Group2.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group3.bash
run_slurm_smcpp_fonio_cultivated_cv_Group3.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group4.bash
run_slurm_smcpp_fonio_cultivated_cv_Group4.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group5.bash
run_slurm_smcpp_fonio_cultivated_cv_Group5.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Group6.bash
run_slurm_smcpp_fonio_cultivated_cv_Group6.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample10_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample10_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample1_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample1_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample2_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample2_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample3_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample3_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample4_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample4_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample5_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample5_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample6_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample6_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample7_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample7_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample8_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample8_tp.bash
 
 
run_slurm_smcpp_fonio_cultivated_cv_Sample9_tp.bash
run_slurm_smcpp_fonio_cultivated_cv_Sample9_tp.bash
 
 
run_smcpp_fonio_wild_cv_NEW.bash
run_smcpp_fonio_wild_cv_NEW.bash
 
 

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This repository contains portion of codes used to launch the smc++ analysis for fonio genome resequencing data. Provided are scripts launched to built a genome mask for the analysis (see paper for details), lists of individuals for which analysis was made and scripts submitted to a SLURM workload manager in a HPC environment.

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