- recipe plassembler
Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
- Homepage:
- License:
MIT / MIT
- Recipe:
- package plassembler¶
- versions:
1.6.2-0,1.6.1-0,1.6.0-0,1.5.1-0,1.5.0-0,1.4.1-1,1.4.1-0,1.4.0-0,1.3.0-0,1.6.2-0,1.6.1-0,1.6.0-0,1.5.1-0,1.5.0-0,1.4.1-1,1.4.1-0,1.4.0-0,1.3.0-0,1.2.0-0,1.1.0-0,1.0.0-1,1.0.0-0,0.1.5-0,0.1.4-0,0.1.3-0,0.1.2-0- depends alive-progress:
>=3.0.1- depends biopython:
>=1.76- depends canu:
2.2- depends chopper:
>=0.5.0- depends click:
>=8.0.0- depends dnaapler:
>=0.4.0- depends fastp:
>=0.18.0- depends flye:
>=2.9- depends loguru:
>=0.5.3- depends mash:
>=2.2- depends minimap2:
>=2.11- depends pandas:
>=1.4.2- depends pysam:
>=0.16.0- depends python:
>=3.8,<3.10- depends pyyaml:
>=6.0- depends raven-assembler:
>=1.8- depends requests:
>=2.25.1- depends samtools:
>=0.15.0- depends unicycler:
>=0.4.8- 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 plassembler and update with:: mamba update plassembler
To create a new environment, run:
mamba create --name myenvname plassembler
with
myenvnamebeing 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/plassembler:<tag> (see `plassembler/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/plassembler/README.html)
