A snakemake script to run core snp phylogeny to a batch of fasta files using Snippy.
1.Reference genome:fasta format was only tested right now.
Change the full path of your reference genome in autosnippy.smk file
2.fasta.txt:a file containing the samples and their full path.Such as:
a the/full/path/of/a.fasta
b the/full/path/of/b.fasta
3.Change the number after "--cpus" to the suitable number of your computer or server.
Just type
snakemake -s autosnippy.smk -c 16
and wait.
All will be done.
1.Snippy The main software of this small script, if you use this script for your work, please cite Snippy in your paper or study.