recipe genomics-data-index

Indexes genomics data (nucleotide variants, kmers, MLST) for fast querying of features.






package genomics-data-index

(downloads) docker_genomics-data-index



depends bamtools:

depends bcftools:


depends bedtools:

depends biocommons.seqrepo:

depends biopython:


depends click:

depends click-config-file:

depends coloredlogs:

depends ete3:

depends fasttree:

depends htslib:


depends iqtree:

depends jinja2:

depends minimap2:

depends numpy:

depends packaging:

depends pandas:


depends pathvalidate:

depends pybedtools:

depends pymysql:

depends pyqt:

depends pyroaring:

depends pytest:

depends python:


depends pyyaml:

depends requests:

depends requests-html:

depends samtools:


depends scikit-bio:

depends scipy:


depends snakemake:

depends snpeff:

depends sourmash:

depends sqlalchemy:

depends vcfpy:

depends zipp:



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 genomics-data-index

and update with::

   mamba update genomics-data-index

To create a new environment, run:

mamba create --name myenvname genomics-data-index

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<tag>

(see `genomics-data-index/tags`_ for valid values for ``<tag>``)

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