README.md

# hqSNP_WGS

Pipeline to identify high quality SNPs in whole genome sequence of bacteria. Pipeline trim the data using bbduk as followed in the script (snippy_pipeline.sh), run the RaXML for phylogenetic tree onstruction.

Create conda environment.Packages are listed in the environment.yaml file.

conda env create -f environment.yaml

Prepare snippy file for multiple files run (More detail, please follow snippy tutorial-https://github.com/tseemann/snippy)

snippy-multi input.tab --ref Reference.gbk --cpus 16 > runme.sh

Run the script

Make sure the input files (fastq.gz), a reference (name.gb) are in the same working directory

snippy_pipeline.sh

Run the output file in iTOL to make a phylogentic tree

RAxML_bootstrap.NAME_bootstrap