- 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:
- License:
BSD-3-Clause
- Recipe:
- package clair3¶
- versions:
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
,1.0.10-1
,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 bzip2:
>=1.0.8,<2.0a0
- depends cffi:
1.14.4.*
- depends libcurl:
>=7.87.0,<8.0a0
- depends libgcc:
>=13
- depends liblzma:
>=5.6.3,<6.0a0
- depends libstdcxx:
>=13
- 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 zstd:
- requirements:
- additional platforms:
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>``)
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)