Tools for analysing usher results.
des.json is lineage designations and is
downloaded from https://nextstrain.org/charon/getDataset?prefix=staging/nextclade/sars-cov-2/ .
It is used to tune some of the ill-defined branches on usher tree(usually caused by deletions) to their correct form.
reference_seq.txt is SARS-Cov-2 reference seq.
To analyse, run
python analyse.py --usher usher.json --important-threshold 2
usher.json is the json file downloaded from usher (upload fasta to https://genome.ucsc.edu/cgi-bin/hgPhyloPlace to get it)
important-threshold is the threshold of uploaded seqs for important branches to display.
The program will automatically filter out all seqs of the 2 forms: 1：singlet seqs with >5 reversions compared with a designated lineage 2：undesignated lineages with (spike/Orf9b/new stop codon/start codon removed).
Packages required:
json
argparse
copy
Add highlighted lineage features to highlight samples with too many reversions, branches with additional undesignated Spike or Orf9b mutation, or branches with early stop signal/start codon destroyed.
Link to view important seqs on the most recent uploads (date replaced to the most recent date and num refers to number of seqs (1:0-1000, 2:1000-2000 etc)): Currently updating every 3-5 days.
Example for seqs 0-1000 at 7-10(referring to 7-6~7-9 seqs on GISAID)： https://nextstrain.org/fetch/raw.githubusercontent.com/xz-keg/Lineage-Detector/main/2024-7-10-1.json?branchLabel=Spike%20mutations&f_userOrOld=highlighted%20sample
Tech Report: Lineage Detector: Efficient Tool for Detecting New SARS-Cov-2 Lineages https://www.biorxiv.org/content/10.1101/2024.11.01.621557v1