Scripts and workflows used to produce figures

Prerequisites

• Nextflow
• Singularity

General commands

The file run.sh indicates commands to run.

Inferring the tree

First, modify the gofasta.config file, especially the following attributes to adapt to the local hpc environment

• fastqueue = 'common,dedicated'
• fastqos= '--qos=fast'
• normalqueue = 'cnrvir'
• normalqos = '-A cnrvir'
• longqueue = 'cnrvir'
• longqos = '-A cnrvir'
• bigmemqueue = 'common'
• executor

Then run nextflow:

nextflow run gofasta.nf -c gofasta.config

It will produce the output files in the results folder, in particular:

• context.aligned.fasta_masked.fasta.gz: The masked sequences of the global contextual samples
• gisaid_pangolin.tsv: Pangolin annotation of all the sequences
• bootaligns/*: Bootstrap alignments
• boottrees/*: Bootstrap trees
• align.treefile: Phylogenetic tree
• align_fbp.treefile: Phylogenetic tree with bootstrap supports
• ba286.aligned.fasta_closest.txt: The name of the closest sequences to BA.2.86 queries
• ba286.aligned.fasta_closest_unique_sequences.fasta.gz: The sequences of the closest sequences to BA.2.86 queries
• ba286.aligned.fasta_closest_unique_sequences.fasta_masked.fasta.gz: The masked sequences of the closest sequences to BA.2.86 queries

Producing the figures

R (v4.3.0)

> source("figures/lineageStats.R")
> source("figures/plot_mutations.R")

DOI