coreSNPs

MAG: metagenome-assembled genomes

In this repo, we start with assembled and taxonomically annotated contigs from sunbeam pipeline:

• assess the draft assemblies quatlify using checkm.

• pangenome analysis using roary.

• extract core genes using in-house R script

• calculate SNPs for each core gene using snp-sites

• calcuate hamming distance

Install coresnps Conda environment

conda env update --name=coresnps --quiet --file env.yml

Assess assemblies quality

Checkm requires python2.7 and we also take care of the precalcualted checkm-database in the checkm_dataset rule.

snakemake --configfile config.yml _run_checkm --use-conda --cores 8

Pangenome analysis

snakemake --configfile config.yml run_roary --cores 8