recipe verkko

A hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate (HiFi, ONT Duplex, ONT HERRO) and long (ONT UL) reads.

Homepage:

https://github.com/marbl/verkko

Documentation:

https://github.com/marbl/verkko/blob/v2.2.1/README.md

License:

CC0

Recipe:

/verkko/meta.yaml

Links:

doi: 10.1038/s41587-023-01662-6, usegalaxy-eu: verkko

package verkko

versions:

2.2.1-0,  2.2-0,  2.1-0,  2.0-0,  1.4.1-0,  1.4-0,  1.3.1-0,  1.3-0,  1.2-0, 

2.2.1-0,  2.2-0,  2.1-0,  2.0-0,  1.4.1-0,  1.4-0,  1.3.1-0,  1.3-0,  1.2-0,  1.1-1,  1.1-0,  1.0-3,  1.0-2,  1.0-1,  1.0-0

depends _openmp_mutex:

>=4.5

depends biopython:

depends bwa:

>=0.7.17

depends findutils:

>=4.6.0

depends graphaligner:

>=1.0.19

depends gsl:

>=2.7,<2.8.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=12

depends libgomp:

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends mashmap:

>=3.0.6

depends minimap2:

>=2.28

depends networkx:

>=2.6.3

depends parasail-python:

>=1.3.3

depends perl:

>=5.6

depends pulp:

<=2.7.0

depends pysam:

depends python:

>=3.9

depends samtools:

>=1.17

depends seqtk:

depends snakemake-minimal:

>=7.8.0,<8.0

depends winnowmap:

>=2.0

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 verkko

and update with::

   mamba update verkko

To create a new environment, run:

mamba create --name myenvname verkko

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/verkko:<tag>

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

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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/verkko/README.html)