├── Custom_cluster_demo └── custom_cls.txt ├── Download_DB_script ├── akk_db.sh ├── cae_db.sh ├── ecoli_db.sh ├── lcr_db.sh ├── mtb_db.sh ├── pre_db.sh ├── sau_db.sh └── sep_db.sh ├── LICENSE ├── Output_Example ├── GCA_000144385_5X_GCF_008868325_5X │ ├── C4 │ │ └── StrainVote.report │ └── final_report.txt └── GCF_003812785 │ ├── C4 │ └── StrainVote.report │ └── final_report.txt ├── README.md ├── Sim_Data.zip ├── Sim_Data_mul.zip ├── StrainScan.py ├── StrainScan_build.py ├── StrainScan_subsample.py ├── Test_genomes.zip ├── environment.yaml ├── environment_candidate.yaml ├── library ├── Build_kmer_sets_unique_region_lasso_test_allinone_cls_sp.py ├── Build_kmer_sets_unique_region_lasso_test_allinone_sp.py ├── Build_kmer_sets_unique_region_lasso_test_allinone_sp_Seperate.py ├── Build_kmer_sets_unique_region_lasso_test_allinone_sp_mtb.py ├── Build_overlap_matrix_sp.py ├── Build_overlap_matrix_sp_jellyfish.py ├── Build_tree.py ├── Build_tree_mem.py ├── Check_overlap_matrix_sp.py ├── Cluster.py ├── IDENTIFY_Sep.py ├── IDENTIFY_V1.py ├── Recls_withR_new.py ├── Unique_kmer_detect.py ├── Unique_kmer_detect_direct.py ├── Vote_Strain_L2_Lasso_new_sp.py ├── __pycache__ │ ├── Build_kmer_sets.cpython-37.pyc │ ├── Build_kmer_sets_unique_region.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test_allinone.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test_allinone_cls.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test_allinone_para.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test_allinone_sp.cpython-37.pyc │ ├── Build_kmer_sets_unique_region_lasso_test_allinone_sp_mtb.cpython-37.pyc │ ├── Build_overlap_matrix_sp.cpython-37.pyc │ ├── Build_tree.cpython-37.pyc │ ├── Cluster.cpython-36.pyc │ ├── Cluster.cpython-37.pyc │ ├── Cluster_matrix.cpython-37.pyc │ ├── Get_Union_KmerSets.cpython-37.pyc │ ├── KrakenBuild.cpython-37.pyc │ ├── Recls_withR.cpython-37.pyc │ ├── Recls_withR_new.cpython-37.pyc │ ├── Unique_kmer_detect.cpython-37.pyc │ ├── Unique_kmer_detect_direct.cpython-36.pyc │ ├── Unique_kmer_detect_direct.cpython-37.pyc │ ├── Vote_Cls_KK.cpython-37.pyc │ ├── Vote_Cls_KK.cpython-38.pyc │ ├── Vote_Strain_L1_Lasso_cls.cpython-37.pyc │ ├── Vote_Strain_L1_Lasso_cls.cpython-38.pyc │ ├── Vote_Strain_L2.cpython-37.pyc │ ├── Vote_Strain_L2_Lasso.cpython-37.pyc │ ├── Vote_Strain_L2_Lasso_new.cpython-37.pyc │ ├── Vote_Strain_L2_Lasso_new_sp.cpython-37.pyc │ ├── Vote_Strain_L2_Lasso_withu.cpython-37.pyc │ ├── Vote_Strain_ini.cpython-37.pyc │ ├── generate_SNV_matrix_with_GSAlign.cpython-37.pyc │ ├── generate_SNV_matrix_with_Pairwise2.cpython-37.pyc │ ├── identify.cpython-37.pyc │ ├── identify_cluster.cpython-37.pyc │ ├── identify_cluster_u.cpython-37.pyc │ ├── identify_strains_L1_Pscan_new.cpython-37.pyc │ ├── identify_strains_L1_Pscan_new.cpython-38.pyc │ ├── identify_strains_L2_Enet_Pscan.cpython-37.pyc │ ├── identify_strains_L2_Enet_Pscan_new.cpython-37.pyc │ ├── identify_strains_L2_Enet_Pscan_new_sp.cpython-37.pyc │ ├── identify_strains_L2_Enet_Pscan_withu.cpython-37.pyc │ ├── identify_strains_L2_Lasso_Pscan.cpython-37.pyc │ ├── identify_strains_L2_ridge_Pscan.cpython-37.pyc │ ├── msa_polish_with_kalign.cpython-37.pyc │ ├── msa_polish_with_mafft.cpython-37.pyc │ ├── select_rep.cpython-37.pyc │ └── test.cpython-37.pyc ├── build │ ├── lib.linux-x86_64-3.7 │ │ └── seqpy.cpython-37m-x86_64-linux-gnu.so │ └── temp.linux-x86_64-3.7 │ │ └── seqpy.o ├── dashing_s128 ├── generate_kmer_with_sts_con_block.py ├── hier.R ├── identify.py ├── identify_cluster_u.py ├── identify_low_depth.py ├── identify_low_mem.py ├── identify_strains_L2_Enet_Pscan_new_sp.py ├── identify_strains_L2_Enet_Pscan_new_sp_et.py ├── jellyfish-linux ├── mannual_convert_sp.py ├── select_rep.py ├── seqpy.c ├── seqpy.cpython-37m-x86_64-linux-gnu.so └── setup.py └── test_run.sh /Custom_cluster_demo/custom_cls.txt: 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