HSV1

Phylogeny analysis for HSV-1 glycoproteins

This repo analyzes the current HSV-1 sequences that have been sequenced by running a snakemake pipeline that downloads sequences based a list of accessions, processes the sequences, and constructs a phylogenetic Nextstrain tree that can be viewed using Auspice.

Analysis performed by Caleb Carr.

Genbank accessions

To download the accessions, go to NCBI Virus and click Search by virus. In the Search by virus name or taxonomy box, enter Human alphaherpesvirus 1 (Herpes simplex virus type 1), taxid:10298 and hit enter. Then click the Download option, select Accession List and Nucleotide options and hit Next. On the next page, select Download All Records and hit Next. On the next page, select Accession with version and click Download. Sequences are downloaded from the list of accessions because more information is extracted from the genbank file during the download process. The current accession list was downloaded on September 10th, 2024.

Outgroup for rooting tree

The HSV-2 reference genome (accession: NC_001798.2) is used to root the tree but the sequence is removed from the tree and alignments.

Snakemake pipeline

The pipeline can be run automatically using snakemake to run Snakefile, which reads its configuration from config.yaml. The results of the automated steps are placed in Results.

To run these steps, first build the conda environment, which installs the necessary programs. First install conda. Then build the environment.

conda env create -f environment.yml

Then activate the conda environment with:

conda activate HSV1_nextstrain_analysis

and then run the pipeline on a computing cluster with slurm, which uses the configuration specified in cluster.yml:

sbatch run_snakemake_cluster.bash

Organization of this repo

• Configure: Contains the files needed to configure the pipeline including the config.yaml and Input_Data which contains list of accessions, reference genomes, and outgroup references.
• Rules: Contains the snakemake rules used to run the pipeline.
• Scripts: Contains the custom python scripts used for part of the analysis.
• Results: Contains the automatically generated results from the pipeline analysis.
• auspice: Contains the automatically generated nextstrain tree files from the pipeline analysis. Note these files are the manually copied to the outermost auspice directory for final visualization.