Outliers in the Dengue Dataset

[Rohit-Satyam]

The following Accessions were found as the outlier sequences by Hill et al 2024 in her recent publication (The list below is the courtesy of Suraj Jagtap on the paper. These sequences were found to emanate from re sequencing of commonly used virus stocks.

@j23414 Do you guys plan to retain them or remove them. Kindly let me know (I see that there are some nextclade people on the paper).

MW828678.1
MT076932.1
MT076933.1
MT076934.1
MT076935.1
MK506262.1
KU094071.1
KM204119.1
EU848545.1
MZ284953.1
MZ285732.1
MF576311.1
MW945433.1
MT076937.1
MH613984.1
MH613985.1
MH613986.1
MK506264.1
MK506263.1
KU094070.1
KM204118.1
KF704358.1
KF704357.1
KF704354.1
KF704355.1
KJ918750.1
KF704356.1
HQ891023.1
HQ891024.1
GQ398268.1
FJ906959.1
FJ390389.1
EU854293.1
MZ285058.1
KY586699.1
OP809583.1
LT996912.1
MT076948.1
MK506265.1
JN697379.1
KM190936.1
MW793460.1
MT076955.1
KY586824.1
KY586825.1
MW793459.1
KY586823.1
KY586826.1
MK506266.1

[j23414]

Hi @Rohit-Satyam! Would you feel comfortable submitting a PR to remove these outliers from the live build? Mostly it involves adding them to this exclude list

• https://github.com/nextstrain/dengue/blob/main/phylogenetic/config/exclude.txt

We usually leave off the version number (e.g. MK506266.1 -> MK506266) and add a comment on reasoning, for line example:

MK506266 # Outlier according to publication Hill et al, 2024 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/)

[Rohit-Satyam]

Okay @j23414 . I see 9 of them are already there. So I will add rest 40 of the accessions

[j23414]

Thanks @Rohit-Satyam ! Closing this since #84 merged