├── .DS_Store ├── ._.DS_Store ├── README.md ├── data ├── interpatient │ ├── fastANI │ ├── filter_seqs.py │ ├── interpatient_snps.txt │ ├── mar20_filtered.aln │ ├── mar20_filtered.treefile │ ├── mar20_filtered_seqs.fna │ ├── ncbi_mar20.fna │ └── nucleotide_diversity.txt ├── intrapatient │ ├── 02_04_2020_SRA_parsed_info.csv │ ├── 04202020_SRA_parsed_info_v2.csv │ ├── 27_03_2020_tables │ │ ├── COVID_gene_coverage_v2.csv │ │ ├── COVID_genome_coverage.csv │ │ ├── COVID_positional_coverage_v2.csv.gz │ │ └── COVID_raw_SNVs.csv │ ├── COVID_SNPs_v1.csv │ ├── COVID_gene_coverage_v2.csv │ ├── COVID_gene_coverage_v4.csv │ ├── COVID_genes_positional_v2.csv.gz │ ├── COVID_genes_positional_v4.csv │ ├── COVID_genes_table_v4.csv │ ├── COVID_genome_coverage.csv │ ├── COVID_genome_coverage_v1.csv │ ├── COVID_genome_coverage_v2.csv │ ├── SNPs │ │ ├── bbtools_snps.csv.gz │ │ ├── bcftools_snps.csv.gz │ │ ├── freebayes_snps.csv.gz │ │ ├── iVar_snps.csv.gz │ │ ├── inStrain_snps.csv.gz │ │ ├── lofreq_snps.csv.gz │ │ ├── onecodex_snps.csv.gz │ │ └── varscan_snps.csv.gz │ ├── SRA_metadata_v1.csv │ ├── all_filtered_snvs.tsv │ ├── high_quality_snps1.tsv │ └── high_quality_snps2.tsv └── reference_genome │ ├── COVID_genes_positional_v2.csv │ ├── COVID_genes_table_v2.tsv │ ├── COVID_genes_table_v3.tsv │ ├── README.md │ ├── reference.fna │ └── reference.gff ├── notebooks ├── Covid_1_annotateGenes_1_v4.ipynb ├── Covid_3_loadInStrain_4.ipynb ├── Covid_3_loadInStrain_5_04022020.ipynb ├── Covid_3_loadInStrain_5_04202020.ipynb ├── Covid_4_analyze_1_microdiversity_3.ipynb ├── Covid_4_analyze_1_microdiversity_5_04022020.ipynb ├── Covid_4_analyze_1_microdiversity_6_04202020.ipynb ├── Covid_4_analyze_2_SNVs_2_04022020.ipynb ├── Covid_5_pipeline_2_04022020.ipynb ├── Covid_5_pipeline_3_04202020.ipynb ├── interpatient_pi.ipynb └── interpatient_snps.ipynb └── results ├── 27_03_2020_figures ├── CodonNormMicrodiversity_min_50_27_03_2020.png ├── Coverage_distribution_27_03_2020.png ├── GeneMicrodiversity_RankOrder_27_03_2020.png ├── Microdiversity_distribution_27_03_2020.png ├── NomalizedMicrodiversity_distribution_27_03_2020.png ├── QC_boxplots_27_03_2020.png └── QC_boxplots_v1.png ├── CodonMicrodiversity_min_1000_v2.png ├── CodonMicrodiversity_min_50_v2.png ├── CodonMicrodiversity_min_50_v3.png ├── CodonNormMicrodiversity_min_50_02_04_2020.png ├── CodonNormMicrodiversity_min_50_v3.png ├── CoverageDistrubution_Center_ID_v2.png ├── GeneMicrodiversity_RankOrder_02_04_2020.png ├── GeneMicrodiversity_RankOrder_27_03_2020.png ├── GeneMicrodiversity_RankOrder_Coverage_v2.png ├── GeneMicrodiversity_RankOrder_interIntra_02_04_2020.png ├── GeneMicrodiversity_RankOrder_interIntra_27_03_2020.png ├── GeneMicrodiversity_RankOrder_interIntra_v2.png ├── GeneMicrodiversity_RankOrder_v2.png ├── GeneMicrodiversity_scatter_interIntra_02_04_2020.png ├── GeneMicrodiversity_scatter_interIntra_27_03_2020.png ├── GeneMicrodiversity_scatter_interIntra_v2.png ├── 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