- recipe biodiff
exact comparison of biological sequences
- Homepage:
- License:
GPLv3+
- Recipe:
biodiff is a variant caller that determines the exact differences between two biological sequences. It can operate on DNA and protein sequences, as long as they are in fasta format. The sequences to be compared must have the same fasta header (up to the first whitespace). If the reference and query each have only one sequence, however, the header need not match and the comparison will be done, but a warning will be emitted. Output is in the Variant Call Format.
- package biodiff¶
- Versions:
0.2.2-6,0.2.2-5,0.2.2-4,0.2.2-3,0.2.2-2,0.2.2-1,0.2.2-0- Depends:
on libgcc
>=13on perl
- 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 biodiff
to add into an existing workspace instead, run:
pixi add biodiff
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 biodiff
Alternatively, to install into a new environment, run:
conda create -n envname biodiff
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/biodiff:<tag>
(see biodiff/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¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/biodiff/README.html)
