- recipe mity
Mity is a bioinformatic analysis pipeline designed to call mitochondrial SNV and INDEL variants from Whole Genome Sequencing (WGS) data.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
- Links:
biotools: mity, doi: 10.26502/jbsb.5107074
*Mity* can: - identify very low-heteroplasmy variants, even <1% heteroplasmy when there is sufficient read-depth (eg >1000x) - filter out common artefacts that arise from high-depth sequencing - easily integrate with existing nuclear DNA analysis pipelines (mity merge) - provide an annotated report, designed for clinicians and researchers to interrogate
- package mity¶
- Versions:
2.0.1-0,2.0.0-0,1.2.0-0,1.1.0-0- Depends:
on freebayes
>=1.2on gsort
>=0.1.4on numpy
on pandas
on pysam
on python
>=3.10on pyyaml
on scipy
on vcf2pandas
on vcfanno
on xlsxwriter
- 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 mity
to add into an existing workspace instead, run:
pixi add mity
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 mity
Alternatively, to install into a new environment, run:
conda create -n envname mity
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/mity:<tag>
(see mity/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/mity/README.html)
