https://github.com/silask/metagenome-qc

Snakmake-workflow for qc
https://github.com/silask/metagenome-qc

Last synced: about 1 month ago
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Snakmake-workflow for qc

• Host: GitHub
• URL: https://github.com/silask/metagenome-qc
• Owner: SilasK
• License: mit
• Created: 2024-01-15T08:17:17.000Z (11 months ago)
• Default Branch: main
• Last Pushed: 2024-07-05T08:24:27.000Z (6 months ago)
• Last Synced: 2024-11-02T15:02:51.818Z (about 2 months ago)
• Language: Python
• Size: 48.8 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Snakemake workflow: ``

[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)

[![GitHub actions status](https://github.com///workflows/Tests/badge.svg?branch=main)](https://github.com///actions?query=branch%3Amain+workflow%3ATests)

A Snakemake workflow for ``

## Usage

The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=%2F).

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 `` and `` everywhere in the template (also under .github/workflows) with the correct `` name and owning user or organization.

* Replace `` with the workflow name (can be the same as ``).

* Replace `` 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 `` and `` 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