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:

https://github.com/HKU-BAL/Clair

License:

AGPLv3

Recipe:

/clair/meta.yaml

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:

• bcftools

• intervaltree

• matplotlib-base

• numpy >=1.17,<1.18

• parallel

• pigz

• pip

• pypy3.6

• pysam

• python >=3,<3.8

• python-blosc

• samtools

• tensorflow >=1.13,<1.14

• vcflib

• zstd

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install clair

and update with:

conda update clair

or use the docker container:

docker pull quay.io/biocontainers/clair:<tag>

(see clair/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

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