Lineage assignments using phylogenetic placement/UShER is superior to machine learning methods

This repository contains the New York City Public Health Laboratory local datasets for the paper, "Lineage assignments using phylogenetic placement/UShER is superior to machine learning methods." COVID samples were collected between August 01, 2021 and November 30, 2021.

Files:

• pipeline.txt - Overview of pipeline and associated scripts

Data files:

Fasta files can be directly inputted into any software that takes multi-fasta format such as pangolin or Nextclade. This is not to be confused with multiple sequence alignment (MSA), which aligns the sequences against each other instead of just listing them.

• nyc_failed_aug-nov2021.fasta - Multi-Fasta file containing 469 genome consensus sequences for SARS-CoV-2 that had N >10%.
• nyc_passed_aug-nov2021.fasta.xz - Compressed fasta file containing genome consensus sequences for SARS-CoV-2 that had N <10%.
  • To uncompress with the xz-utils package, the command is unxz nyc_passed_aug-nov2021.fasta.xz
• ca_nyc_mafft.alignment.fasta.xz - Compressed MSA created by MAFFT
  • To uncompress with the xz-utils package, the command is unxz ca_nyc_mafft.alignment.fasta.xz
• pango_consensus_ca_nyc.aligned_sept8_2023_masked_maple034inferenceJC_noAncertaintyAssignment_reRooted_nexusTree.tree - MAPLE tree used for lineage assignment validation
• 60k_public_meta.tsv - NCBI metadata for 2021 global dataset
• 2022-global-episet.pdf - GISAID supplemental table to access 2022 global dataset

Script files:

• compareLineages.py - Python script to compare pangolin lineages to MAPLE tree
• comparison_script_w_ami.py - Python script to calculate Adjusted Mutual Information
• snp_scorpio-comparisons.sh - Bash script to preprocess SNP distance matrix
• snp_scorpio-comparisons.Rmd - R script to analyze SNP distance matrix data and scorpio
• tables_and_violin_plots.R - R script to create visualization to compare genome coverage to reassignment and other tables
• sankey_plots.R - R script to create visualization to look at lineage stability
• Files catalogueing new lineages during the study periodbetween pangolin versions which we considered as permitted changes
  • expected.13.14.tsv
  • expected.14.15.tsv
  • expected.15.16.tsv
  • expected.2021-11-09_v1.2.133.tsv

Supplemental files:

• Supplementary_table_1.csv
• Supplementary_table_2.csv
• Supplementary_table_3.csv
• Supplementary_table_4.csv
• Supplementary_file_public_60k_pusher_nohash.html - Interactive HTML showing the lineage reassignments across different versions of pUSHER
• Supplementary_file_public_60k_plearn_nohash.html - Interactive HTML showing the lineage reassignments across different versions of pangoLEARN

Authors

• Adriano de Bernardi Schneider
• Michelle Su
• Angie S. Hinrichs
• Jade Wang
• Helly Amin
• John Bell
• Debra A. Wadford
• Ainde O'Toole
• Emily Scher
• Marc D. Perry
• Yatish Turakhia
• Nicola De Maio
• Andrew Rambaut
• Scott Hughes
• Russ Corbett-Detig