├── LICENSE ├── README.md ├── clustering-phasing ├── Snakefile ├── add_unphased_nodes_tofile.py ├── cluster_allnodes.py ├── cluster_phasing.py ├── compute_graphstats.py ├── config.yaml ├── split_files.py ├── write_haplo_colors.py ├── write_nodes_to_haplotypes.py ├── write_paths.py └── write_threaded_paths.py ├── coverage-analysis ├── Snakefile ├── smk_coverage_altus.py ├── sum_node_cov_5kb.py └── write_dosages.py ├── filter_and_replace.py ├── kmer-counting ├── CMakeLists.txt ├── CMakeLists.txt~ ├── Snakefile ├── Snakefile~ ├── argumentparser.cpp~ ├── config.yaml ├── config_offspring.json ├── environment.yml ├── evaluate_kmers.py ├── filter_and_replace.py ├── merge_countfiles_allnodes.py ├── polyassembly_findkmers.cpp~ ├── src │ ├── CMakeLists.txt │ ├── CMakeLists.txt~ │ ├── argumentparser.cpp │ ├── argumentparser.hpp │ ├── jellyfishkmercounter.cpp │ ├── jellyfishkmercounter.hpp │ ├── polyassembly_countkmers.cpp │ ├── polyassembly_countkmers.cpp~ │ ├── polyassembly_findkmers.cpp │ ├── polyassembly_findkmers.cpp~ │ ├── sequence_mers.hpp │ ├── uniquekmers.cpp │ └── uniquekmers.hpp └── test-data │ ├── testkmerfile.fa │ ├── testread.fa │ └── testshortreadfile.fa ├── merge_countfiles_allnodes.py └── sum_node_cov_5kb.py~ /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rebeccaserramari/polyploid-potato-assembly/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rebeccaserramari/polyploid-potato-assembly/HEAD/README.md -------------------------------------------------------------------------------- /clustering-phasing/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rebeccaserramari/polyploid-potato-assembly/HEAD/clustering-phasing/Snakefile 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