This repository is a snakemake workflow for aligning many genome assemblies to a reference genome using my preferred parameters, tools, and outputs.
This workflow is also convenient for making inputs for my visualization tool SafFire.
snakemake --configfile .test/config.yaml
snakemake --configfile config/config.yaml
snakemake --configfile config/config.yaml ideogram
For arm Macs (MX) many bioconda packages are not available, but I have had luck with the following:
CONDA_SUBDIR=osx-64 snakemake --configfile config/config.yaml
Running alignment and gene conversion identification pipeline:
snakemake \
--configfile config/config_asm20.yaml \
--cores $threads \
--use-conda \
-p \
gene_conversion
Information on where to download the input assemblies can be found on Zenodo.
Config files for human assemblies:
config/config_asm20.yaml
config/table.asm.tbl
Config files for the Clint PTR assembly:
config/clint.yaml
config/clint.asm.tbl