From 5d6291ddec8200d79828326eaaac3deed5c826cf Mon Sep 17 00:00:00 2001 From: james hadfield Date: Thu, 29 Aug 2024 16:35:15 +1200 Subject: [PATCH] Add 3 outliers to cattle-flu build The metadata of the dropped strains warrants further investigation, but dropping for now as they completely throw the tree. First identified on SPHERES slack, see for more. --- .../dropped_strains_h5n1-cattle-outbreak.txt | 6 ++++++ 1 file changed, 6 insertions(+) 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