recipe longstitch

A genome assembly correction and scaffolding pipeline using long reads

Homepage:

https://bcgsc.ca/resources/software/longstitch

Documentation:

https://github.com/bcgsc/longstitch

License:

GPL-3.0

Recipe:

/longstitch/meta.yaml

Links:

https: :https:`//doi.org/10.1101/2021.06.17.448848`

package longstitch

(downloads) docker_longstitch

versions:

1.0.5-0,  1.0.4-1,  1.0.4-0,  1.0.3-0,  1.0.2-0,  1.0.1-2,  1.0.1-1,  1.0.1-0

depends arcs:

>=1.2.2

depends links:

1.8.7

depends make:

depends ntlink:

depends python:

depends samtools:

depends tigmint:

>=1.2.4

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 longstitch

and update with::

   mamba update longstitch

To create a new environment, run:

mamba create --name myenvname longstitch

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/longstitch:<tag>

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

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Link to this page

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