- recipe medaka
A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks.
- Homepage:
- Documentation:
https://github.com/nanoporetech/medaka/blob/v2.0.1/README.md
- License:
OTHER / MPL-2.0
- Recipe:
- Links:
usegalaxy-eu: medaka_consensus, usegalaxy-eu: medaka_consensus_pipeline, usegalaxy-eu: medaka_variant, usegalaxy-eu: medaka_variant_pipeline, biotools: medaka
- package medaka¶
- versions:
2.0.1-0,2.0.0-0,1.11.3-0,1.11.2-0,1.11.1-0,1.11.0-0,1.10.0-0,1.8.0-0,1.7.2-1,2.0.1-0,2.0.0-0,1.11.3-0,1.11.2-0,1.11.1-0,1.11.0-0,1.10.0-0,1.8.0-0,1.7.2-1,1.7.2-0,1.7.1-1,1.7.1-0,1.7.0-0,1.6.1-2,1.6.1-1,1.6.1-0,1.6.0-0,1.5.0-2,1.5.0-1,1.5.0-0,1.4.4-0,1.4.3-0,1.4.2-0,1.4.1-0,1.3.3-0,1.3.2-0,1.3.0-0,1.2.6-1,1.2.6-0,1.2.5-0,1.2.3-0,1.2.2-0,1.2.1-1,1.2.1-0,1.2.0-0,1.1.3-0,1.1.2-0,1.1.1-0,1.0.3-1,1.0.3-0,1.0.1-0,1.0.0-0,0.12.1-0,0.11.5-1,0.11.5-0,0.11.4-0,0.11.3-0,0.11.2-0,0.11.1-0,0.11.0-1,0.11.0-0,0.10.1-0,0.10.0-1,0.10.0-0,0.9.2-0,0.9.1-0,0.9.0-0,0.8.1-1,0.8.1-0,0.8.0-0,0.7.1-1,0.7.0-1,0.7.0-0,0.6.5-0,0.6.4-0,0.6.2-0,0.6.0-0,0.5.2-0- depends bcftools:
>=1.14- depends bzip2:
>=1.0.8,<2.0a0- depends cffi:
- depends grpcio:
- depends h5py:
- depends htslib:
>=1.14- depends htslib:
>=1.21,<1.22.0a0- depends intervaltree:
- depends libcurl:
>=8.8.0,<9.0a0- depends libgcc:
>=12- depends libzlib:
>=1.2.13,<2.0a0- depends mappy:
- depends minimap2:
>=2.17- depends numpy:
>=1.21.0,<2.0.0- depends ont-fast5-api:
- depends openssl:
>=3.3.2,<4.0a0- depends parasail-python:
- depends pyabpoa:
- depends pysam:
>=0.16.0.1- depends pyspoa:
>=0.2.1- depends python:
>=3.10,<3.11.0a0- depends python-edlib:
- depends python_abi:
3.10.* *_cp310- depends pytorch:
>=2.3,<2.4- depends requests:
- depends samtools:
>=1.14- depends tqdm:
- depends wurlitzer:
- depends xz:
>=5.2.6,<6.0a0- 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 medaka and update with:: mamba update medaka
To create a new environment, run:
mamba create --name myenvname medaka
with
myenvnamebeing 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/medaka:<tag> (see `medaka/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/medaka/README.html)
