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rsv_step3
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README.md
README.md
 
 

README.md

Phylogenetic trees of Respiratory Syncytial Virus

This repository builds trees of the Respiratory Syncytial Virus (RSV) subtypes -A and -B from full genome sequences. The final trees are viewable at https://nextstrain.org/groups/blab/rsv/A and https://nextstrain.org/groups/blab/rsv/B, and are built in multiple steps using a modified Nextstrain pipeline. The steps (outlined below) are used to assign subtype -A or -B to each genome, and to build alignments and trees that are consistent with the large duplication events that occur within the G gene.

Step 0:

  • Download all RSV data from ViPR as vipr_download.fasta
  • Run format_downloaded_genomes.ipynb to format dates and output rsv.fasta
  • Run Snakefile in rsv_step0/
  • Use label_rsv_subtypes.ipynb to separate the unaligned rsv.fasta file into RSV-A and RSV-B fasta files based off the tree
  • Use extract_gene_fastas.ipynb to create separate fasta files for the whole genome, G and F genes

Step 1:

  • Run Snakefile in rsv_step1/ to construct separate trees for RSV-A and RSV-B using a reference sequences that contains the G gene duplication

Step 2:

  • Separate sequences with the duplication from those without using separate_strains_with_dup.ipynb
  • Run Snakefile in rsv_step2/ to build two trees for each subtype: one includes only sequences with the G duplication and is aligned to a reference containing the duplication, the other contains only sequences without the G duplication and is aligned to the same reference but with the duplication removed

Step 3:

  • Use separate_strains_with_dup.ipynb to add a column to the metadata_{subtype}.tsv files saying whether that strain has the G gene duplication or not (this will be used as a color_by option). This also saves the metadata_{subtype}.tsv file into rsv_step3/data/
  • Run make_step3_alignment.ipynb to add placeholders to the aligned sequences that do not have the duplication and to concatenate the alignment files produced in Step 2. This will save aligned_{subtype}_all.fasta to rsv_step3/data/
  • Run merge_insertion_tsvs.ipynb to retrieve information about insertions that were inferred during the alignment in Step 2. These will be used to label insertions on branches
  • Run Snakefile in rsv_step3/ to output the final tree
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