/snakemap

Read-mapping against the contig catalogue from metagenomics by illumina and nanopore

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

Snakemake workflow: snakemap

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A Snakemake workflow for snakemap

A snakemake workflow for read-mapping against the contig catalogue from metagenomics by illumina and nanopore

Usage

  1. Init
python init.py -i /path/to/illumina_fqs -n /path/to/nanopore_fqs -w /path/to/workdir
  1. Run
snakemake all -j6 --snakefile /path/to/Snakefile --configfile /path/to/config.yaml --directory /path/to/workdir --use-conda