diff --git a/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt b/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt index 224701a..c9e96bc 100755 --- a/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt +++ b/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt @@ -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 diff --git a/ingest/build-configs/ncbi/defaults/host-map.tsv b/ingest/build-configs/ncbi/defaults/host-map.tsv index 4919d2f..3cb92ca 100644 --- a/ingest/build-configs/ncbi/defaults/host-map.tsv +++ b/ingest/build-configs/ncbi/defaults/host-map.tsv @@ -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