Usher Analyse Tool, welcome for usage and suggestions.

[xz-keg]

Hi, I wrote an open-sourced usher analyse tool that can automatically highlight important lineages in usher-processed jsons. Hope it can help everyone find and analyse new lineages more quickly, especially for those multiple lineage ones.

Welcome for usage and suggestions.

Repo: https://github.com/aviczhl2/usher_analyse_tool

For fast access to highlighted lineages for daily new sequences: (Most recent 1000 seqs by sample date uploaded in the last 24 hrs) https://nextstrain.org/fetch/raw.githubusercontent.com/aviczhl2/usher_analyse_tool/main/usher-2.json?branchLabel=Spike%20mutations&f_userOrOld=highlighted%20sample

(1000~2000 seqs by sample date uploaded in the last 24 hrs) https://nextstrain.org/fetch/raw.githubusercontent.com/aviczhl2/usher_analyse_tool/main/usher-3.json?branchLabel=Spike%20mutations&f_userOrOld=highlighted%20sample

(2000~3000 seqs by sample date uploaded in the last 24 hrs) https://nextstrain.org/fetch/raw.githubusercontent.com/aviczhl2/usher_analyse_tool/main/usher-4.json?branchLabel=Spike%20mutations&f_userOrOld=highlighted%20sample

Highlight criteria: 1: Sequences with >=5 reversions compared with a designated reference. (Shall check for potential recombinant)

2: Branches with undesignated S or Orf9b mutations, or any new stop codon/start codon removal, with >=3 seqs in a 1000-seq batch, or 2 seqs from different regions.