Snakemake pipeline for reference-guided genome assembly. Requires conda and snakemake installed. The pipeline handles the rest of the dependencies at runtime.
Each pipeline run needs an updated config.yml and samples.tsv file. Templates are provided, as well as an example with more detailed instructions
Example run on a small dataset:
git clone https://github.com/louiejtaylor/frieman_genomes
cd frieman_genomes/example/
snakemake all_summarize --use-conda --conda-frontend conda -p --snakefile ../Snakefile --configfile example_config.yml --cores 1
Alternately, on a cluster (Slurm in the below example) the command could look like this (using snakemake<8.0):
snakemake all_summarize --use-conda --conda-frontend conda -p --snakefile ../Snakefile --configfile example_config.yml --jobs 1 --cores 1 --latency-wait 30 --cluster "sbatch --mem 10G -c {threads} "
Used by Frieman lab members for genome assembly of sequenced laboratory stocks.