├── .DS_Store ├── .gitignore ├── NCBI_tax_id ├── ncbi_tax_id.ipynb └── results │ ├── TaxID_gtdb-ncbi_v214.xlsx │ └── TaxID_gtdb-ncbi_v220.xlsx ├── NCBI_vs_GTDB ├── Gtdb_ncbi_compare_plot.ipynb ├── Gtdb_tax_ncbi_names.ipynb ├── README.md ├── Tax_gtdb.xlsx └── results │ ├── GTDB_all_species.xlsx │ ├── Tax_gtdb-ncbi_v207.xlsx │ ├── Tax_gtdb-ncbi_v214.xlsx │ ├── Tax_gtdb-ncbi_v220.xlsx │ └── gtdb_nacbi_matches.png ├── Program_Comparison ├── Binners_comparison.ipynb ├── Mapurify_compare_one_smpl.ipynb ├── README.md └── cut_long_reads.py ├── RAD ├── 2022_Abundance-Prevalence.ipynb ├── 2022_ReadsNumb_vs_ContigsStats.ipynb ├── 2022_kraken_Domain_microbiome_composition.ipynb ├── 2022_kraken_Phylum_microbiome_composition.ipynb ├── 2022_kraken_top_rank.ipynb ├── 2022_kraken_top_species.ipynb ├── 2022_reads_number_Path.sh └── README.md ├── README.md ├── ShortReads_from_LongReads ├── README.md ├── cut_long_reads.py ├── cut_zero_reads.py ├── input │ └── sample.fasta └── short_reads_stats.sh ├── checkM1_vs_checkM2 ├── CheckM12_comparison.xlsx └── checkM1_vs_checkM2.ipynb ├── gtdb_vizualization ├── .DS_Store ├── 2022_gtdb_vizualization.ipynb ├── README.md ├── input │ ├── ar53_taxonomy_r207.tsv │ ├── ar53_taxonomy_r214.tsv │ ├── bac120_taxonomy_r207.tsv │ └── bac120_taxonomy_r214.tsv └── results │ ├── release207_GTDB_all_class.html │ ├── release207_GTDB_all_class.png │ ├── release207_GTDB_arch.html │ ├── release207_GTDB_arch_genus.html │ ├── release207_GTDB_arch_genus.png │ ├── release207_GTDB_bac120.html │ ├── release207_GTDB_bac_genus.html │ ├── release207_GTDB_bac_genus.png │ ├── release214_GTDB_all_class.html │ ├── release214_GTDB_all_class.png │ ├── release214_GTDB_arch.html │ ├── release214_GTDB_arch.png │ ├── release214_GTDB_bac120.html │ ├── release214_GTDB_bac120.png │ └── release220_GTDB_all_class.html ├── gunc_visualization ├── .DS_Store ├── GUNC_results.ipynb ├── input │ ├── .DS_Store │ ├── V40FOF_metabat.1_sub.contig_assignments.tsv │ ├── V40FOF_metabat.1_sub_CG.txt 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