This respository documents the scripts used to analyse data for the paper:

Jackson B, et al. Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic. Submitted

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It is organised into the following subdirectories (in alphabetical order), which represent the file structure used in the original analyses, but note that the sequences and their associated metadata are not included in this repository:

3seq_weighted_background

• the command used to run 3SEQ

background

• scripts to handle the comprehensive background sequence dataset (of non-recombinant sequences)

bams

• scripts to investigate the raw read data for the recombinants

bams_ambig

• scripts to investigate the raw read data for the mixtures

figures

• scripts to generate figures for the manuscript

geography

• scripts to investigate the presence of other lineages in the geographic locations of the putative recombinants

groupA_neighbours_tree

• scripts and metadata to generate the phylogenetic tree for the Group A transmission chain + parental context

mask_1

• scripts to carry out the first mask and search for candidate parental sequences by genetic similarity for the different regions of the recombinant genomes

mask_2

• scripts to carry out the final mask and search for candidate parental sequences by genetic similarity for the different regions of the recombinant genomes

recombinant_genomes

• scripts to handle the recombinant genomes

scripts

• miscellaneous python scripts which were called elsewhere in the repository

weighted background

• scripts to generate and analyse the weighted random sample of background (non-recombinant) sequences from the UK

weighted_background_phylo_incong

• scripts for running the phylogenetic incongruence analysis, and the resulting phylogenetic trees