├── LICENSE ├── README.md ├── analysis ├── plot_RNA_levels.py ├── plot_bootstrap_results.py ├── plot_coverage.py ├── plot_kallisto_vs_salmon.py ├── plot_raw_predictions.py ├── plot_results_biobot.py ├── plot_results_clinical.py ├── plot_results_cov_exp.py └── plot_sequence_diversity.py ├── auxiliary_data ├── WHO_variants_2021-10-06.json ├── adapters.fa ├── primers.bed └── reference_set_03_2021.txt ├── benchmarking ├── create_benchmarks.py ├── create_error_benchmarks.py ├── create_uneven_depth.py ├── evaluate_abundances.py ├── evaluate_error.py └── run_kallisto_ref_sets.sh ├── dependencies.txt ├── example ├── SARS-CoV-2-NC_045513.fasta ├── input_1.fastq ├── input_2.fastq ├── metadata.tsv └── sequences.fa ├── manuscript ├── README.md ├── make_figures.sh ├── output_abundances_v1.py ├── preprocess_references_v1.py ├── run_kallisto_ref_sets_v1.sh ├── run_kallisto_uneven_cov_exp.sh ├── run_kallisto_v1.sh └── select_samples_v1.py ├── pipeline ├── call_variants.sh ├── cleanup_ref_dir.sh ├── index_database.py ├── output_abundances.py ├── preprocess_references.py ├── run_kallisto.sh ├── run_salmon.sh ├── select_samples.py └── trim_reads.sh └── supplement ├── amplicon_bias_exp └── amplicon_bias_exp.sh ├── error_rate_exp └── Snakefile ├── ref_count_bias_exp ├── exp1 │ ├── 1_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 2_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 3_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 4_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 5_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 6_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 7_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 8_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── 9_voc │ │ ├── Snakefile │ │ └── config.yaml │ ├── analysis.ipynb │ ├── downsample_voc.py │ ├── results │ │ ├── results_0.1_voc_2_exp.pdf │ │ └── results_3.pdf │ └── utils.py └── exp2 │ ├── 10_seq │ └── Snakefile │ ├── 18_seq │ ├── Snakefile │ ├── benchmarks_nonshuffled │ │ └── ww_BA.1vBA.2 │ │ │ ├── BA.1_EPI_ISL_10223811_50.0x1.aln │ │ │ ├── BA.1_EPI_ISL_10223811_50.0x1.fq │ │ │ ├── BA.1_EPI_ISL_10223811_50.0x2.aln │ │ │ ├── BA.1_EPI_ISL_10223811_50.0x2.fq │ │ │ ├── background_50.0x1.aln │ │ │ ├── background_50.0x1.fq │ │ │ ├── background_50.0x2.aln │ │ │ ├── background_50.0x2.fq │ │ │ ├── metadata.tsv │ │ │ └── sequences.fasta │ └── config.yaml │ ├── 1_seq │ └── Snakefile │ ├── 2_seq │ └── Snakefile │ ├── 3_seq │ └── Snakefile │ ├── 4_seq │ └── Snakefile │ ├── 5_seq │ └── Snakefile │ ├── 6_seq │ └── Snakefile │ ├── 7_seq │ └── Snakefile │ ├── 8_seq │ └── Snakefile │ ├── 9_seq │ └── Snakefile │ ├── analysis.ipynb │ ├── analysis_edit_distance │ ├── NC_045512.2.fasta │ ├── analysis.ipynb │ ├── ed_res.csv │ ├── ed_res_ba1ba2.csv │ ├── metadata_filtered_10.tsv │ ├── scripts.txt │ ├── sequences.bam │ ├── sequences.bam.bai │ ├── sequences_filtered_10.fasta │ ├── sequences_trimmed.fasta │ └── trim_seq.py │ ├── downsample_voc.py │ ├── results │ ├── perLineagevariationbias_exp1_0threshold.pdf │ └── results_4.pdf │ └── utils.py ├── sequence_similarity_exp ├── 12_mutations │ ├── Snakefile │ └── config.yaml ├── 15_mutations │ ├── Snakefile │ └── config.yaml ├── 18_mutations │ ├── Snakefile │ └── config.yaml ├── 21_mutations │ ├── Snakefile │ └── config.yaml ├── 24_mutations │ ├── Snakefile │ └── config.yaml ├── 27_mutations │ ├── Snakefile │ └── config.yaml ├── 30_mutations │ ├── Snakefile │ └── config.yaml ├── 3_mutations │ ├── Snakefile │ └── config.yaml ├── 6_mutations │ ├── Snakefile │ └── config.yaml ├── 9_mutations │ ├── Snakefile │ └── config.yaml ├── analysis.ipynb ├── results │ ├── results.pdf │ ├── results.png │ └── results_fixed_title.pdf ├── sequences │ ├── SARS-CoV-2-NC_045513.fasta │ ├── all_sequences.fasta │ ├── all_sequences_2.fasta │ ├── metadata.tsv │ ├── metadata12m.tsv │ ├── metadata15m.tsv │ ├── metadata18m.tsv │ ├── metadata1m.tsv │ ├── metadata21m.tsv │ ├── metadata24m.tsv │ ├── metadata27m.tsv │ ├── 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