Package Recipe 'cerberus-mg' — Bioconda documentation

recipe cerberus-mg

Three-headed host removal for metagenomic data: assembly, profiling and privacy-scrubbed outputs from one run.

Homepage:: iowa69/cerberus
License:: MIT / MIT
Recipe:: /cerberus-mg/meta.yaml
Links:: doi: 10.5281/zenodo.20258069

Cerberus is an opinionated all-in-one host-decontamination pipeline that produces three outputs from a single run: a paired-end assembly-ready FASTQ pair (conservative — a pair is dropped only when both mates map to the host), a single merged FASTQ for taxonomic profiling (aggressive — the pair is dropped as soon as either mate maps), and a privacy-scrubbed output for public release, from which host reads are removed by three mechanisms in series: a Kraken2 host database, a bbduk human k-mer pass, and minimap2 alignment against a masked T2T-CHM13v2.0 + HLA reference.

Because all three mechanisms derive from the same reference assemblies, Cerberus reports the measured residual host removal per mechanism rather than asserting that no host reads remain. Every run writes an HTML report with the resolved parameters, per-stage read accounting and verification of each output file.

Works on Illumina paired-end short reads, ONT long reads, and PacBio HiFi/CLR, autotuning its parameters from a prescan of the input.

package cerberus-mg#

Versions:

0.2.1-0, 0.1.1-0

Depends:

on aria2
on bbmap >=39.0
on bowtie2 >=2.5
on fastp >=0.24
on fastplong >=0.2
on kraken2 >=2.1.3
on minimap2 >=2.28
on pigz
on python >=3.10
on samtools >=1.20
on tqdm >=4.66
on winnowmap >=2.03
on zstd >=1.5

Additional platforms:

Installation#

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi#

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install cerberus-mg

to add into an existing workspace instead, run:

pixi add cerberus-mg

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda#

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install cerberus-mg

Alternatively, to install into a new environment, run:

conda create -n envname cerberus-mg

with envname being the name of the desired environment.

Container#

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/cerberus-mg:<tag>

(see cerberus-mg/tags for valid values for <tag>).

Integrated deployment#

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page#

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/cerberus-mg/README.html)