Nextstrain repository for African swine fever virus

This repository contains three workflows for the analysis of African swine fever virus data:

• scripts/ - Removes sequences that are missing dates or strain names
• rules/ - Parse and Index sequences to create required files for Nextstrain build
• Snakefile - Filter sequences, align, construct phylogeny and export for visualization

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools (if you don't already have Nextstrain installed!)

Quickstart

Clone github repo

git clone https://github.com/mattparkerls/asf.git
cd asf/

Download African swine fever sequences from NCBI Virus

• recommended filters: Sequence Length > 150000, Sequence Type = GenBank, Collection Date = as narrow a time period as possible

Put sequences.fasta file from NCBI in /data folder

Run the default phylogenetic workflow (build may take several hours depending on how many sequences you have)

nextstrain build .
nextstrain view .

Nextstrain Documentation

• Running a pathogen workflow