taxonomy workflow

Build a phylogeny with FastTree based on a concatenated alignment of 103 marker genes identified with checkM. Can include local fasta files as well as genomes downloaded from the NCBI with Assembly Finder (https://github.com/metagenlab/assembly_finder).

input

See templates folder

• config file
• assembly finder table
• local genome(s) table

execution

snakemake --snakefile Snakefile --configfile config.yaml --use-conda --conda-prefix ~/miniconda3/ --use-singularity --cores 20 plots/phylo.svg

example output figure: phylogeny of the family Orbaceae