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sars-cov-2.yaml
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sars-cov-2.yaml
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---
name: SARS-CoV-2
general:
aligner: "bwa"
input:
reference: "{VPIPE_BASEDIR}/../resources/sars-cov-2/NC_045512.2.fasta"
metainfo_file: "{VPIPE_BASEDIR}/../resources/sars-cov-2/metainfo.yaml"
gff_directory: "{VPIPE_BASEDIR}/../resources/sars-cov-2/gffs/"
protocols_file: "{VPIPE_BASEDIR}/../resources/sars-cov-2/primers.yaml"
inserts_bedfile: "{VPIPE_BASEDIR}/../resources/sars-cov-2/primers/v3/nCoV-2019.insert.bed"
primers_bedfile: "{VPIPE_BASEDIR}/../resources/sars-cov-2/primers/v3/nCoV-2019.primer.bed"
primers_file: "{VPIPE_BASEDIR}/../resources/sars-cov-2/primers/v3/nCoV-2019.tsv"
primers_fasta: "{VPIPE_BASEDIR}/../resources/sars-cov-2/primers/v3/ARTIC_v3.fasta"
phylogeny_data: "{VPIPE_BASEDIR}/../resources/sars-cov-2/phylogeny/selected_covid_sequences.fasta"
genes_gff: "{VPIPE_BASEDIR}/../resources/sars-cov-2/gffs/Genes_NC_045512.2.GFF3"
snv:
consensus: false
lofreq:
consensus: false