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NBISweden/nf-core-aMeta

Open in GitHub Codespaces GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

Introduction

NBISweden/nf-core-aMeta is a bioinformatics pipeline for identifying and authenticating microbial sequences in ancient DNA shotgun metagenomics samples. It is a Nextflow/nf-core reimplementation of the original Snakemake workflow aMeta, described in Pochon, Bergfeldt et al., Genome Biology 2023 (doi:10.1186/s13059-023-03083-9).

Starting from shotgun sequencing reads, the pipeline:

  1. Trims adapters and filters short reads with Cutadapt, with QC before and after trimming via FastQC and MultiQC
  2. Performs k-mer-based taxonomic classification with KrakenUniq and screens for common microbial pathogens
  3. Aligns reads with Bowtie2 and profiles deamination patterns with mapDamage2
  4. Performs Lowest Common Ancestor (LCA) alignment with MALT
  5. Authenticates and validates candidate ancient microbial species with MaltExtract

Each of these analysis stages beyond the initial QC/classification (MapDamage2, the full MALT/authentication pipeline, and Krona taxonomy plots) can be individually toggled on or off. The output includes per-sample, per-species authentication scores and diagnostic plots (deamination profile, coverage evenness, read length distribution, PMD scores, and more), alongside abundance matrices from both KrakenUniq and MALT.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run NBISweden/nf-core-aMeta \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

NBISweden/nf-core-aMeta was originally written by Mahesh Binzer-Panchal, based on the original aMeta Snakemake pipeline written by Zoé Pochon.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.