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

(downloads) docker_clair3

versions:
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, 

1.0.10-0,  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 bzip2:

>=1.0.8,<2.0a0

depends cffi:

1.14.4.*

depends libcurl:

>=7.87.0,<8.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends numpy:

depends openssl:

1.1.1.*

depends openssl:

>=1.1.1w,<1.1.2a

depends parallel:

20191122.*

depends pigz:

depends pypy3.6:

depends pytables:

depends python:

>=3.9,<3.10.0a0

depends python_abi:

3.9.* *_cp39

depends samtools:

1.15.1.*

depends tensorflow:

2.8.0.*

depends whatshap:

1.7.*

depends xz:

>=5.2.6,<6.0a0

depends zstd:

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 clair3

and update with::

   mamba update clair3

To create a new environment, run:

mamba create --name myenvname clair3

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/clair3:<tag>

(see `clair3/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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