This repository contains a snakemake pipeline that runs the PHASM de novo genome assembler for several synthetic genomes. Using the provides Conda environment file is the easiest way to install all dependencies.
- Python >= 3.5
- Snakemake >= 3.11
- DAZZ_DB / DALIGNER
- NumPy
- SciPy
- Pandas
- matplotlib
- networkx
- samtools
- pysam
- simlord
Clone the repository, and move into that directory. Then create the conda environment and run the pipeline.
conda env create -f environment.yml
source activate phasm
# Run the whole pipeline
snakemake --cores 16 all