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cattle-flu updates #90

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merged 2 commits into from
Aug 29, 2024
Merged

cattle-flu updates #90

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6237092
Update host-map TSV
jameshadfield Aug 29, 2024
5d6291d
Add 3 outliers to cattle-flu build
jameshadfield Aug 29, 2024
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6 changes: 6 additions & 0 deletions config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt
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Expand Up @@ -17,6 +17,12 @@ A/domesticcat/NewMexico/24-009116-001/2024
# These strains are basal to the outbreak and we exclude them to avoid low-confidence DTA reconstruction.
A/Peregrinefalcon/California/24-005915-001/2024

# These three cattle strains are hundreds of mutations diverged from the outbreak - perhaps due to poor sequencing?
# Perhaps they are another introduction? Dropping for now
A/CATTLE/USA/24-022332-005/2024
A/CATTLE/USA/24-015672-001/2024
A/CATTLE/USA/24-022332-007/2024

# These strains represent diversity that's significantly outgrouped relative to cattle outbreak
A/americancrow/Iowa/24-006634-001/2024
A/AmericanCrow/USA/24-004479-001-original/2024
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2 changes: 2 additions & 0 deletions ingest/build-configs/ncbi/defaults/host-map.tsv
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@@ -1,8 +1,10 @@
# Check for bird codes in https://www.carolinabirdclub.org/bandcodes.html
# Note that the first column in this TSV is case insensitive
Accipitridae Avian
alpaca Nonhuman Mammal
american crow Avian
AMERICAN ROBIN Avian
Turdus migratorius Avian
american wigeon Avian
Anas platyrhynchos Avian
Anatidae Avian
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