recipe lrtk

This is a unified and versatile ToolKit for analyzing Linked-Read sequencing data.






package lrtk

(downloads) docker_lrtk



depends aquila:

depends bcftools:

depends bedtools:

depends bowtie2:

depends bwa:

depends fastp:

depends freebayes:

depends gatk:

depends hapcut2:

depends megahit:

depends metabat2:

depends parallel:

depends picard:

depends python:

depends r-ade4:

depends r-base:

depends r-clustersim:

depends r-factoextra:

depends r-ggforce:

depends r-ggplot2:

depends r-proxy:

depends r-vegan:

depends tabix:

depends vcflib:

depends vcftools:



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 lrtk

and update with::

   mamba update lrtk

To create a new environment, run:

mamba create --name myenvname lrtk

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<tag>

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

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