├── .gitignore ├── README.md ├── Snakefile ├── cfg.py ├── envs ├── anaconda.pipeline-env.yaml ├── anaconda.snakemake-env.yaml └── anaconda.snakemake-env_MacOSX.yaml ├── install_MacOSX.sh ├── install_Ubuntu16_04.sh ├── libraries └── README.md ├── output ├── consensus-genomes │ ├── README.md │ ├── VI1-minion-miseq-comparison-aln.fasta │ ├── VI4-minion-miseq-comparison-aln.fasta │ ├── ZIKA_COL_good.fasta │ ├── ZIKA_COL_good_porechopUpdate.fasta │ ├── ZIKA_COL_partial.fasta │ ├── ZIKA_COL_partial_porechopUpdate.fasta │ ├── ZIKA_COL_poor.fasta │ ├── ZIKA_COL_poor_porechopUpdate.fasta │ ├── ZIKA_USVI_good.fasta │ ├── ZIKA_USVI_good_porechopUpdate.fasta │ ├── ZIKA_USVI_partial.fasta │ ├── ZIKA_USVI_partial_porechopUpdate.fasta │ ├── ZIKA_USVI_poor.fasta │ └── ZIKA_USVI_poor_porechopUpdate.fasta └── depth-coverage │ ├── README.md │ ├── figures │ ├── usvi-library1 │ │ ├── Coverage-Overlap-NB01-NB07.png │ │ ├── Coverage-Overlap-NB02-NB08.png │ │ ├── Coverage-Overlap-NB03-NB09.png │ │ ├── Coverage-Overlap-NB04-NB10.png │ │ ├── Coverage-Overlap-NB05-NB11.png │ │ └── Coverage-Overlap-NB06-NB12.png │ └── usvi-library3 │ │ ├── Coverage-Overlap-NB01-NB07.png │ │ ├── Coverage-Overlap-NB02-NB08.png │ │ ├── Coverage-Overlap-NB03-NB09.png │ │ ├── Coverage-Overlap-NB04-NB10.png │ │ ├── Coverage-Overlap-NB05-NB11.png │ │ └── Coverage-Overlap-NB06-NB12.png │ └── refs │ ├── ZikaReferenceGenome.fasta │ ├── ZikaReferenceGenome.fasta.amb │ ├── ZikaReferenceGenome.fasta.ann │ ├── ZikaReferenceGenome.fasta.bwt │ ├── ZikaReferenceGenome.fasta.pac │ └── ZikaReferenceGenome.fasta.sa ├── pipeline ├── Dockerfile ├── README.md ├── basecall │ ├── README.md │ ├── clear_workspace.py │ ├── count_ratios.py │ ├── distribute_albacore.py │ ├── grab_1000_fast5s.py │ ├── prep_lib.py │ ├── remove_tmp.py │ └── subdivide.py ├── data-schema.md ├── demux │ ├── cat_demux_fastas.py │ ├── fix.py │ ├── merge.py │ └── split_1d_library.py ├── docker-minion-pipeline-DEPRECATED.md ├── docker-notes.md ├── docker_README.md ├── metadata │ ├── PHE_v2.amplicons.bed │ ├── chik_primal_KP164568.bed │ ├── v2_500.amplicons.ver1.bed │ ├── v2_500.amplicons.ver2.bed │ ├── v3_300.amplicons.ver1.bed │ └── v3_300.amplicons.ver2.bed ├── miseq_pipeline │ ├── README.md │ ├── amplicons_prefix.fa │ ├── zika_dc_2016.fa │ └── zika_dc_2016.nix ├── refs │ ├── KJ776791.2.fasta │ ├── KJ776791.2.fasta.amb │ ├── KJ776791.2.fasta.ann │ ├── KJ776791.2.fasta.bwt │ ├── KJ776791.2.fasta.fai │ ├── KJ776791.2.fasta.pac │ ├── KJ776791.2.fasta.sa │ ├── KJ776791.2.gb │ ├── Zika_Africa.fasta │ ├── Zika_Brazil.fasta │ ├── Zika_DC.fa │ ├── Zika_FP.fasta │ └── barcodes │ │ └── barcodes.fasta ├── run.py ├── scripts │ ├── INSTALL │ ├── README.md │ ├── align_trim.py │ ├── depth_coverage.R │ ├── depth_process.py │ ├── fasta_to_consensus_1d.sh │ ├── fasta_to_consensus_2d.sh │ ├── get-alignment.py │ ├── illumina │ │ ├── README.md │ │ ├── align_reads │ │ │ ├── Snakefile │ │ │ ├── cluster.json │ │ │ └── run_pipeline.sh │ │ ├── db │ │ │ └── zika_dc_2016.fa │ │ └── get_coverage │ │ │ ├── Snakefile │ │ │ ├── cluster.json │ │ │ ├── plot_coverage.py │ │ │ └── run_pipeline.sh │ ├── make_test_set.py │ ├── margin_cons.py │ ├── marginalign.sh │ ├── nanopolish_header.py │ ├── pdf_tree.py │ ├── pipeline.py │ ├── runs.py │ ├── runstats.py │ └── vcftagprimersites.py └── test_on_library8.md ├── protocols ├── README.md ├── amplicon-generation.md ├── cleanup-and-amplicon-quantification.md ├── demultiplex-investigation.md ├── minion-flowcell-loading.md ├── minion-library-prep-1Dchemistry.md ├── minion-library-prep-2Dchemistry.md ├── minion-running-commands.md ├── miseq-library-preparation.md ├── primer-pool-recipe.md ├── viral-rna-extraction.md └── zika-multiplex-primers.xls ├── samples ├── README.md ├── runs.tsv └── samples.tsv └── seq-validation ├── KJ776791.2.fasta ├── VI1-seq-comparisons-aligned.fasta ├── VI19-seq-comparisons-aligned.fasta ├── VI19_SNPcall_comparisons.tsv ├── VI1_SNPcall_comparisons.tsv ├── VI2-seq-comparisons-aligned.fasta ├── VI2_SNPcall_comparisons.tsv ├── VI3-seq-comparisons-aligned.fasta ├── VI3_SNPcall_comparisons.tsv ├── VI4-seq-comparisons-aligned.fasta ├── VI41-ref-nanopolish-comp-aligned.fasta ├── VI41.consensus.polished.fasta ├── VI41_SNPcall_comparisons.tsv ├── VI42.consensus.fasta ├── VI4_SNPcall_comparisons.tsv ├── VI5-seq-comparisons-aligned.fasta ├── VI5_SNPcall_comparisons.tsv ├── assess-interplatform-snp-calling.ipynb └── per-base-error-calculation.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/blab/zika-seq/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/blab/zika-seq/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: 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