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Ingest from INSDC

enhancementNew feature or requestNew feature or request

Status: Open.

#265 In nextstrain/seasonal-flu;

· huddlej opened on Nov 3, 2025

H3N2 sequences classified as J.2.4 in Nextclade appear only as J.2 in my Nextstrain tree

bugSomething isn't workingSomething isn't working

Status: Open.

#254 In nextstrain/seasonal-flu;

· RasmusKoRiis opened on Sep 24, 2025

ingest: prioritize records by available segments

Status: Open.

#253 In nextstrain/seasonal-flu;

· joverlee521 opened on Sep 17, 2025

Ingest workflow for CDC titer data

Status: Open.

#249 In nextstrain/seasonal-flu;

· joverlee521 opened on Aug 23, 2025

Switch builds to use new ingest outputs

Status: Open.

#234 In nextstrain/seasonal-flu;

· joverlee521 opened on May 29, 2025

Add back our ability to exclude specific sites from tree builders in the workflow with <code>tree_exclude_sites</code>

bugSomething isn't workingSomething isn't working

Status: Open.

#232 In nextstrain/seasonal-flu;

· huddlej opened on May 23, 2025

Sunset private.nextflu.org

Status: Open.

#214 In nextstrain/seasonal-flu;

· joverlee521 opened on Feb 12, 2025

Address removal of <code>augur export v1</code> for private.nextflu.org builds

Status: Open.

#213 In nextstrain/seasonal-flu;

· joverlee521 opened on Feb 12, 2025

Tree rooting approaches

Status: Open.

#212 In nextstrain/seasonal-flu;

· jameshadfield opened on Feb 11, 2025

Allow users to define custom nucleotide coordinate offsets for clades for custom references

enhancementNew feature or requestNew feature or request

Status: Open.

#210 In nextstrain/seasonal-flu;

· huddlej opened on Feb 11, 2025

Allow users to run the workflow with Nextclade references for multiple segments

enhancementNew feature or requestNew feature or request

Status: Open.

#209 In nextstrain/seasonal-flu;

· huddlej opened on Feb 11, 2025

Add HA1 and NA mutation counts

enhancementNew feature or requestNew feature or request

Status: Open.

#201 In nextstrain/seasonal-flu;

· huddlej opened on Dec 19, 2024