SilasK / Metagenome-QC

Snakmake-workflow for qc

Snakemake workflow: <name>

A Snakemake workflow for <description>

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) sitory and its DOI (see above).

TODO

• Replace <owner> and <repo> everywhere in the template (also under .github/workflows) with the correct <repo> name and owning user or organization.
• Replace <name> with the workflow name (can be the same as <repo>).
• Replace <description> with a description of what the workflow does.
• The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if <owner> and <repo> were correctly set.

I use FastP:

Kraken for decontamination with this index https://zenodo.org/records/8339732

reccomended by Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data View ORCID ProfileMichael B. Hall, View ORCID ProfileLachlan J.M. Coin doi: https://doi.org/10.1101/2023.09.18.558339