recipe merqury

Evaluate genome assemblies with k-mers and more.

Homepage:

https://github.com/marbl/merqury

License:

PUBLIC DOMAIN

Recipe:

/merqury/meta.yaml

Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

package merqury

versions:

1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.1-3,  1.1-2,  1.1-1,  1.1-0,  v1.0-0

depends bedtools:

>=2.29.2

depends gawk:

depends meryl:

1.3.*

depends mscorefonts:

depends openjdk:

>=11.0.1

depends r-argparse:

>=2.0.1

depends r-base:

>=4

depends r-ggplot2:

>=3.3.2,<=3.3.6

depends r-scales:

>=1.1.1

depends samtools:

>=1.10

depends sed:

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 merqury

and update with::

   mamba update merqury

To create a new environment, run:

mamba create --name myenvname merqury

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/merqury:<tag>

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

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