recipe braker2

BRAKER2 is an extension of BRAKER1

Homepage

https://github.com/Gaius-Augustus/BRAKER

License

Other / Artistic License

Recipe

/braker2/meta.yaml

Links

doi: 10.1093/nargab/lqaa108

BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

package braker2

Versions

2.1.6-5,  2.1.6-4,  2.1.6-3,  2.1.6-2,  2.1.6-1,  2.1.6-0,  2.1.5-3,  2.1.5-2,  2.1.5-1, 

2.1.6-5,  2.1.6-4,  2.1.6-3,  2.1.6-2,  2.1.6-1,  2.1.6-0,  2.1.5-3,  2.1.5-2,  2.1.5-1,  2.1.5-0,  2.1.4-1,  2.1.4-0,  2.1.2-2,  2.1.2-1,  2.1.2-0

Depends

• augustus >=3.4.0

• bamtools >=2.5.1

• biopython

• blast >=2.2.31

• cdbtools >=0.99

• diamond >=0.9.24

• exonerate >=2.2.0

• gemoma 1.6.4

• genomethreader >=1.7.0

• makehub

• perl

• perl-app-cpanminus

• perl-class-data-inheritable

• perl-exception-class

• perl-file-homedir

• perl-file-spec

• perl-file-which

• perl-hash-merge

• perl-list-moreutils

• perl-list-util

• perl-logger-simple

• perl-math-utils

• perl-mce

• perl-module-load-conditional

• perl-parallel-forkmanager

• perl-posix

• perl-scalar-util-numeric

• perl-test-pod

• perl-yaml

• python >=3.3

• samtools >=1.7

• spaln >=2.3.3

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install braker2

and update with:

conda update braker2

or use the docker container:

docker pull quay.io/biocontainers/braker2:<tag>

(see braker2/tags for valid values for <tag>)

Notes

• GeneMark software can be used for free, but requires a license file and should be additionally installed on the machine where the BRAKER2 environment is.

• ProtHint software can be used for free, but doesn't allow redistribution and should be additionally installed on the machine where the BRAKER2 environment is.

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