recipe ngspeciesid

Reference-free clustering and consensus forming of long-read amplicon sequencing

Homepage:

https://github.com/ksahlin/NGSpeciesID

License:

GPL-3.0-or-later

Recipe:

/ngspeciesid/meta.yaml

NGSpeciesID is a tool for clustering and consensus forming of long-read amplicon sequencing data (has been used with both PacBio and Oxford Nanopore data). The repository is a modified version of isONclust, where consensus, primer-removal, and polishing feautures have been added.

package ngspeciesid

versions:

0.3.1-0

depends edlib:

>=1.1.2

depends medaka:

>=2.0.1

depends minimap2:

depends parasail-python:

>=1.2.4

depends python:

>=3.10

depends racon:

depends samtools:

depends spoa:

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 ngspeciesid

and update with::

   mamba update ngspeciesid

To create a new environment, run:

mamba create --name myenvname ngspeciesid

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/ngspeciesid:<tag>

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

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