bin/kissnp2
bin/kissreads2
bin/quick_hierarchical_clustering
bin/read_file_names
bin/run_discoSnp++.sh
bin/run_discoSnp++_ML.sh
bin/run_discoSnpRad.sh
discoSnpRAD/COOKBOOK.md
discoSnpRAD/README.md
discoSnpRAD/clustering_scripts/README.md
discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py
discoSnpRAD/clustering_scripts/from_SRC_to_edges.py
discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py
discoSnpRAD/post-processing_scripts/README.md
discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py
discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py
discoSnpRAD/post-processing_scripts/filter_paralogs.py
discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py
discoSnpRAD/post-processing_scripts/vcf2structure.sh
discoSnpRAD/run_discoSnpRad.sh
scripts/ClassVCF_creator.py
scripts/ClassVCF_creator.pyc
scripts/VCF_creator.py
scripts/__pycache__/ClassVCF_creator.cpython-37.pyc
scripts/__pycache__/functionObjectVCF_creator.cpython-37.pyc
scripts/clusters_and_fasta_to_fasta.py_DEPRECATED
scripts/create_IGV_compatible_VCF.sh
scripts/create_filtered_vcf.py
scripts/discoSnp++_to_csv.py
scripts/filterOnBestDP_multiple_variant_at_same_pos.py
scripts/filter_out_using_MAF.py
scripts/filter_out_using_ratio_of_covered_files.py
scripts/format_phased_for_K2000.py
scripts/format_phased_for_clustering.py
scripts/format_phased_variants_for_haplotyping.py
scripts/from_path_to_edges.py
scripts/from_phased_alleles_to_clusters.sh
scripts/functionObjectVCF_creator.py
scripts/functionObjectVCF_creator.pyc
scripts/jenkins/README
scripts/jenkins/tool-discosnp-build-debian7-64bits-gcc-4.7.sh
scripts/jenkins/tool-discosnp-build-macos-10.9.5-gcc-4.2.1.sh
scripts/jenkins/tool-discosnp-release-debian.sh
scripts/k3000/From phased facts to gfa graph.pdf
scripts/k3000/K3000.py
scripts/k3000/K3000_common.py
scripts/k3000/K3000_enhance_gfa.py
scripts/k3000/K3000_fact_haplotypes_to_localized_variant_ids.py
scripts/k3000/K3000_facts_to_fa.py
scripts/k3000/K3000_facts_to_gfa.py
scripts/k3000/K3000_filter_badly_overlapping_variants.py
scripts/k3000/K3000_find_unitig_connected_pairs_of_facts.py
scripts/k3000/K3000_gfa_post_treatment.py
scripts/k3000/K3000_gfa_to_dat.py
scripts/k3000/K3000_gfa_to_fa.py
scripts/k3000/K3000_msr_to_gfa.py
scripts/k3000/K3000_node_ids_to_node_sequences.py
scripts/k3000/K3000_paths_to_fa.py
scripts/k3000/K3000_phased_paths_to_fa.py
scripts/k3000/K3000_working_zone.py
scripts/k3000/K3000_working_zone_no_redundant_edges.py
scripts/k3000/Snakefile
scripts/k3000/compute_pi.py
scripts/k3000/extract_DP_from_vcf.py
scripts/k3000/negative_binomial.py
scripts/k3000/run_K3000.sh
scripts/k3000/sorted_list.py
scripts/k3000/stats.py
scripts/keep_extensions_disco_file.py
scripts/phasing/phased_variants_to_graph_deprecated.py
scripts/redundancy_removal_discosnp.py
scripts/remove_extensions_disco_file.py
scripts/remove_non_biallelic.py
scripts/remove_non_covered_genotypes.py
scripts/run_VCF_creator.sh
scripts/simulations/README.md
scripts/simulations/ill100v4.bad.qual
scripts/simulations/ill100v4.good.qual
scripts/simulations/multiple_samples_simulator.sh
scripts/simulations/random_mut_fasta.py
scripts/simulations/targeted_mut_fasta_corrected.py
scripts/split_multiple_snps.py
scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py
scripts/validation_scripts/eval_disco_one_snp_per_locus.py
scripts/vcf_formatting_functions.py
