Package Recipe 'clair3'

recipe clair3

Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration.

Homepage:: https://github.com/HKU-BAL/Clair3
License:: BSD-3-Clause
Recipe:: /clair3/meta.yaml

package clair3¶

Versions:

1.2.0-0, 1.1.2-0, 1.1.1-0, 1.1.0-0, 1.0.11-0, 1.0.10-1, 1.0.10-0, 1.0.8-2, 1.0.8-1,

1.2.0-0, 1.1.2-0, 1.1.1-0, 1.1.0-0, 1.0.11-0, 1.0.10-1, 1.0.10-0, 1.0.8-2, 1.0.8-1, 1.0.8-0, 1.0.7-1, 1.0.7-0, 1.0.6-0, 1.0.5-0, 1.0.4-3, 1.0.4-2, 1.0.4-1, 1.0.4-0, 1.0.3-0, 1.0.2-0, 1.0.1-0, 1.0.0-1, 1.0.0-0, 0.1.12-6, 0.1.12-5, 0.1.12-4, 0.1.12-2, 0.1.12-1, 0.1.12-0, 0.1.11-6, 0.1.11-5, 0.1.11-4, 0.1.11-3, 0.1.11-2, 0.1.11-1, 0.1.11-0, 0.1.10-0, 0.1.9-0, 0.1.8-0, 0.1.7-0, 0.1.6-0, 0.1.5-0, 0.1.4.2-0, 0.1.4.1-0, 0.1.4-0

Depends:

on bzip2 >=1.0.8,<2.0a0
on cffi
on libcurl >=8.14.1,<9.0a0
on libgcc >=13
on liblzma >=5.8.1,<6.0a0
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on numpy
on openssl >=3.5.1,<4.0a0
on parallel
on pigz
on pytables
on python >=3.10,<3.11.0a0
on python_abi 3.10.* *_cp310
on samtools
on tensorflow <=2.16.0
on whatshap
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 clair3

to add into an existing workspace instead, run:

pixi add clair3

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 clair3

Alternatively, to install into a new environment, run:

conda create -n envname clair3

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/clair3:<tag>

(see clair3/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair3/README.html)