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:

2.4.2-0,  2.4.1-0

depends biopython:

>=1.78

depends blast:

>=2.8

depends diamond:

>=2.0.15

depends lxml:

>=4.9.1

depends mcl:

>=14.137

depends networkx:

>=2.4

depends python:

>=3.7

depends ruamel.yaml:

>=0.15

depends snakemake:

>=7.24

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install ffgc

and update with::

   mamba update ffgc

To create a new environment, run:

mamba create --name myenvname ffgc

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/ffgc:<tag>

(see `ffgc/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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