├── .dockerignore ├── .gitattributes ├── .github ├── CODEOWNERS └── workflows │ ├── pre-commit.yml │ ├── publish-image.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── covid19_call_variants.ont.sh ├── covid19_call_variants.sh ├── data ├── ARTIC │ ├── ERR5284916.ONT.ARTICv3.40k.fastq.gz │ ├── SRR11314339.ARTICv1.100k.fastq.gz │ ├── SRR11314339.ARTICv1.100k.truth.tsv │ └── SRR16298166.fastq.gz ├── README.md ├── twist-target-capture │ ├── RNA_control_spike_in_10_6_100k_reads.fastq.gz │ └── truth.tsv └── wts │ └── SRR11092059_first_1M.fastq.gz ├── environment.yml ├── generate_tsv.py ├── insert_coverage_stats.py ├── jobscript.sh ├── post_process_variants.sh ├── reference ├── ARTIC-V1-nCoV-2019.scheme.bed ├── ARTIC-V1.bed ├── ARTIC-V2-nCoV-2019.scheme.bed ├── ARTIC-V2.bed ├── ARTIC-V3-nCoV-2019.scheme.bed ├── ARTIC-V3.bed ├── ARTIC-V4.bed ├── NC_045512.2.reference.fasta ├── aa_codes.txt ├── annot_table.orfs.txt ├── artic-primers-v1-and-v2.fa ├── data │ └── NC_045512.2 │ │ ├── genes.gbk │ │ ├── genes.gff │ │ └── sequences.fa ├── low_complexity_regions.txt ├── nCoV-2019.reference.fasta ├── nCoV-2019.reference.gbk ├── nCoV-2019.reference.gtf ├── primer_schemes │ └── nCoV-2019 │ │ ├── V1 │ │ ├── nCoV-2019.bed │ │ ├── nCoV-2019.insert.bed │ │ ├── nCoV-2019.primer.bed │ │ ├── nCoV-2019.reference.fasta │ │ ├── nCoV-2019.scheme.bed │ │ └── nCoV-2019.tsv │ │ ├── V2 │ │ ├── nCoV-2019.bed │ │ ├── nCoV-2019.insert.bed │ │ ├── nCoV-2019.primer.bed │ │ ├── nCoV-2019.reference.fasta │ │ ├── nCoV-2019.scheme.bed │ │ └── nCoV-2019.tsv │ │ ├── V3 │ │ ├── nCoV-2019.bed │ │ ├── nCoV-2019.insert.bed │ │ ├── nCoV-2019.primer.bed │ │ ├── nCoV-2019.reference.fasta │ │ ├── nCoV-2019.scheme.bed │ │ └── nCoV-2019.tsv │ │ ├── V4.1 │ │ ├── nCoV-2019.insert.bed │ │ ├── nCoV-2019.reference.fasta │ │ └── nCoV-2019.scheme.bed │ │ └── V4 │ │ ├── README │ │ ├── nCoV-2019.design.fasta │ │ ├── nCoV-2019.insert.bed │ │ ├── nCoV-2019.primer.bed │ │ ├── nCoV-2019.reference.fasta │ │ └── nCoV-2019.scheme.bed ├── snpEffect.config └── vcf_filter.edited.py ├── report.ipynb ├── requirements.txt ├── setup.cfg └── tests ├── conftest.py ├── test_artic.py ├── test_integration.py ├── test_post_process_variants.py ├── test_simulated_data.py ├── test_simulated_data_noindels.py └── test_twist.py /.dockerignore: -------------------------------------------------------------------------------- 1 | data/* 2 | benchmarks/ 3 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/onecodex/sars-cov-2/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/CODEOWNERS: -------------------------------------------------------------------------------- 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