recipe kssd

K-mer substring space decomposition

Homepage:

https://github.com/yhg926/public_kssd

License:

Apache-2.0

Recipe:

/kssd/meta.yaml

Links:

doi: 10.1186/s13059-021-02303-4

Kssd is a command-line tool for large-scale sequences sketching and resemblance- and containment-analysis. It sketches sequences by k-mer substring space sampling/shuffling. It handles DNA sequences of both fasta or fastq format, whether gzipped or not.

package kssd

(downloads) docker_kssd

versions:

2.21-2,  2.21-1,  2.21-0,  1.1-2,  1.1-1,  1.1-0,  1.0-0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

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 kssd

and update with::

   mamba update kssd

To create a new environment, run:

mamba create --name myenvname kssd

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/kssd:<tag>

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

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