recipe medaka

Neural network sequence error correction.

Homepage

https://github.com/nanoporetech/medaka

Documentation

https://nanoporetech.github.io/medaka/index.html

License

OTHER / Mozilla Public License 2.0

Recipe

/medaka/meta.yaml

Links

usegalaxy-eu: medaka_consensus

package medaka

Versions

1.4.3-0,  1.4.2-0,  1.4.1-0,  1.3.3-0,  1.3.2-0,  1.3.0-0,  1.2.6-1,  1.2.6-0,  1.2.5-0, 

1.4.3-0,  1.4.2-0,  1.4.1-0,  1.3.3-0,  1.3.2-0,  1.3.0-0,  1.2.6-1,  1.2.6-0,  1.2.5-0,  1.2.3-0,  1.2.2-0,  1.2.1-1,  1.2.1-0,  1.2.0-0,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.0.3-1,  1.0.3-0,  1.0.1-0,  1.0.0-0,  0.12.1-0,  0.11.5-1,  0.11.5-0,  0.11.4-0,  0.11.3-0,  0.11.2-0,  0.11.1-0,  0.11.0-1,  0.11.0-0,  0.10.1-0,  0.10.0-1,  0.10.0-0,  0.9.2-0,  0.9.1-0,  0.9.0-0,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.7.1-1,  0.7.0-1,  0.7.0-0,  0.6.5-0,  0.6.4-0,  0.6.2-0,  0.6.0-0,  0.5.2-0

Depends

• bcftools >=1.9

• biopython

• bzip2 >=1.0.8,<2.0a0

• cffi

• h5py

• htslib >=1.12,<1.13.0a0

• intervaltree >=3.0.0

• libgcc-ng >=9.3.0

• mappy

• minimap2 >=2.17

• numpy <1.20.0

• ont-fast5-api

• parasail-python

• pysam >=0.16.0.1

• pyspoa

• python >=3.8,<3.9.0a0

• python-edlib

• python_abi 3.8.* *_cp38

• racon >=1.4.13

• requests

• samtools >=1.9

• tensorflow 2.2.*

• whatshap >=0.18

• xz >=5.2.5,<5.3.0a0

• zlib >=1.2.11,<1.3.0a0

Required By

• hpsuissero

• ssuissero

• dragonflye

• artic

Installation

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

conda install medaka

and update with:

conda update medaka

or use the docker container:

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

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

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/medaka/README.html)