Reference alignment workflow

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.

try the test case

snakemake --configfile .test/config.yaml      

an example run script

snakemake --configfile config/config.yaml 

an example run script with ideograms

snakemake --configfile config/config.yaml ideogram 

note on arm Macs

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 

Notes on use of the pipeline in Vollger et al., 2023

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