recipe ffgc

Family Free Genome Comparison (FFGC) workflow

Homepage:

https://gitlab.ub.uni-bielefeld.de/gi/FFGC

Documentation:

https://gitlab.ub.uni-bielefeld.de/gi/FFGC/blob/master/README.md

License:

BSD

Recipe:

/ffgc/meta.yaml

Family Free Genome Comparison (FFGC) is a self-contained workflow system that provides functionality for all steps of a family-free gene order analysis starting from annotated genome sequences.

Family-free methods for gene order analyses do not require prior knowledge of evolutionary relationships between the genes across the studied genomes. This tool features a complete workflow for genome comparison, requiring nothing but annotated genome sequences as input.

Surprisingly, the continuous development of family-free methods recently lead to an integrated method for inferring gene families across several species. FFGC now includes a subworkflow for inferring gene families simultaneously based on gene similarities and family-free genome rearrangements (OrthoFFGCʜ and OrthoFFGCʜ≈ extensions).

FFGC is available for download at our git repository (https://gitlab.ub.uni-bielefeld.de/gi/FFGC) or as a Conda package at Bioconda (https://anaconda.org/bioconda/ffgc).

In general, three major steps are performed: (1) the computation of local sequence alignment scores between genes of two or more gene order sequences using BLAST+ or Diamond; (2) the establishment of gene relationships; and (3) the actual family-free gene order analysis.

package ffgc

(downloads) docker_ffgc

Versions:

2.4.2-1,  2.4.2-0,  2.4.1-0

Depends:

  • on biopython >=1.78

  • on blast >=2.8

  • on diamond >=2.0.15

  • on lxml >=4.9.1

  • on mcl >=14.137

  • on networkx >=2.4

  • on python

  • on ruamel.yaml >=0.15

  • on snakemake >=7.24

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 ffgc

to add into an existing workspace instead, run:

pixi add ffgc

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 ffgc

Alternatively, to install into a new environment, run:

conda create -n envname ffgc

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/ffgc:<tag>

(see ffgc/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.

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