- recipe clair
Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly, and epigenetic mark detection. However, the lack of a highly accurate small variant caller has limited the new technologies from being more widely used. In this study, we present Clair, the successor to Clairvoyante, a program for fast and accurate germline small variant calling, using single molecule sequencing data. For ONT data, Clair achieves the best precision, recall and speed as compared to several competing programs, including Clairvoyante, Longshot and Medaka. Through studying the missed variants and benchmarking intentionally overfitted models, we found that Clair may be approaching the limit of possible accuracy for germline small variant calling using pileup data and deep neural networks.
- Homepage:
- License:
AGPLv3
- Recipe:
- package clair¶
- Versions:
2.1.1-1,2.1.1-0,2.1.0-1,2.1.0-0,2.0.7-0,2.0.6-1,2.0.6-0,2.0.5-1,2.0.5-0,2.1.1-1,2.1.1-0,2.1.0-1,2.1.0-0,2.0.7-0,2.0.6-1,2.0.6-0,2.0.5-1,2.0.5-0,2.0.4-0,2.0.3-0,2.0.2-0,2.0.1-0,2.0.0-0- Depends:
on bcftools
on intervaltree
on matplotlib-base
on numpy
>=1.17,<1.18on parallel
on pigz
on pip
on pypy3.6
on pysam
on python
>=3,<3.8on python-blosc
on samtools
on tensorflow
>=1.13,<1.14on vcflib
on zstd
- 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 clair
to add into an existing workspace instead, run:
pixi add clair
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 clair
Alternatively, to install into a new environment, run:
conda create -n envname clair
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/clair:<tag>
(see clair/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/clair/README.html)
