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Make tree for 450bp of the N gene ("N450") #20

Merged
merged 11 commits into from
Apr 1, 2024
Merged

Make tree for 450bp of the N gene ("N450") #20

merged 11 commits into from
Apr 1, 2024

Commits on Mar 21, 2024

  1. Add reference files for N450 region 

    Reference is comprised of 450bp of the N gene from the same sample that is used for the genome tree (NCBI Accession NC_001498.1).
    @kimandrews
    kimandrews committed Mar 21, 2024
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  2. Prepare N450 sequences for phylogenetic analysis 

    * Add rule to align sequences to N450 reference using nextclade
* Add rule to filter by length, date, country
    @kimandrews
    kimandrews committed Mar 21, 2024
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  3. Construct phylogeny for N450 region

    @kimandrews
    kimandrews committed Mar 21, 2024
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  4. Annotate phylogeny for N450 region

    @kimandrews
    kimandrews committed Mar 21, 2024
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  5. Export phylogeny for N450 region

    @kimandrews
    kimandrews committed Mar 21, 2024
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Commits on Mar 28, 2024

  1. Use --stochastic-resolve option for augur refine

    @kimandrews
    kimandrews committed Mar 28, 2024
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  2. Remove "country" colors from defaults/colors.tsv

    @kimandrews
    kimandrews committed Mar 28, 2024
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  3. Change default display to rooted time-tree

    @kimandrews
    kimandrews committed Mar 28, 2024
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  4. Use --metadata-columns to export "author" in auspice_config.json

    @kimandrews
    kimandrews committed Mar 28, 2024
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  5. Organize builds as directories within results

    @kimandrews
    kimandrews committed Mar 28, 2024
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Commits on Apr 1, 2024

  1. Update Changelog

    @kimandrews
    kimandrews committed Apr 1, 2024
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