From 6f9144f7767c0cac4755c60cd5c069a5d2c4ed6f Mon Sep 17 00:00:00 2001 From: Rohit Satyam Date: Mon, 14 Oct 2024 21:18:07 +0300 Subject: [PATCH] Exclude outlier sequences flagged by Hill et al 2024 (#84) Excluded 40 genomes that were found as outliers due to re-sequencing commonly used viral stocks by Hill et al 2024 Following outlier format reported in [issue 83](https://github.com/nextstrain/dengue/issues/83#issuecomment-2405537358) --- phylogenetic/config/exclude.txt | 40 +++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/phylogenetic/config/exclude.txt b/phylogenetic/config/exclude.txt index 354abee..ad4b0d1 100644 --- a/phylogenetic/config/exclude.txt +++ b/phylogenetic/config/exclude.txt @@ -897,3 +897,43 @@ OR389026 # denv2 many Ns OR389325 # denv2 many Ns OR389023 # denv2 many Ns OR389307 # denv2 many Ns +MK506262 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KU094071 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KM204119 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +EU848545 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MF576311 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MW945433 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MT076937 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MH613984 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MH613985 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MH613986 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MK506264 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MK506263 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KU094070 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KM204118 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KF704358 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KF704357 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KF704354 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KF704355 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KJ918750 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KF704356 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +HQ891023 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +HQ891024 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +GQ398268 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +FJ906959 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +FJ390389 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +EU854293 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KY586699 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +OP809583 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MT076948 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MK506265 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +JN697379 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KM190936 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MW793460 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MT076955 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KY586824 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KY586825 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MW793459 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KY586823 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +KY586826 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/) +MK506266 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/)