recipe nextpolish

Fast and accurately polish the genome generated by noisy long reads

Homepage:

https://github.com/Nextomics/NextPolish

Documentation:

https://nextpolish.readthedocs.io/en/latest

License:

GPL3 / GPL-3.0-or-later

Recipe:

/nextpolish/meta.yaml

Links:

biotools: NextPolish, doi: 10.1093/bioinformatics/btz891

package nextpolish

(downloads) docker_nextpolish

versions:

1.4.1-3,  1.4.1-2,  1.4.1-1,  1.4.1-0

depends bwa:

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends minimap2:

depends paralleltask:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

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 nextpolish

and update with::

   mamba update nextpolish

To create a new environment, run:

mamba create --name myenvname nextpolish

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/nextpolish:<tag>

(see `nextpolish/tags`_ for valid values for ``<tag>``)

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