recipe gpatch

Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Download the github repository for helper scripts to automate GPatch workflows, identify and correct misjoins in the contig assembly, produce dot-plots of patched pseudoassemblies to a reference assembly, and generate chrom.sizes and liftover chains for patched pseudoassemblies."

Homepage:

https://github.com/adadiehl/GPatch.git

License:

MIT / MIT

Recipe:

/gpatch/meta.yaml

package gpatch

(downloads) docker_gpatch

versions:

0.4.0-0,  0.3.8-0,  0.3.6-0,  0.3.5-0,  0.3.4-0

depends biopython:

>=1.84

depends pysam:

>=0.22.1

depends python:

>=3.7,<3.13

requirements:

additional platforms:

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 gpatch

and update with::

   mamba update gpatch

To create a new environment, run:

mamba create --name myenvname gpatch

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/gpatch:<tag>

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

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Link to this page

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