recipe bioconductor-contibait

Improves Early Build Genome Assemblies using Strand-Seq Data



BSD_2_clause + file LICENSE




biotools: contibait, doi: 10.1093/bioinformatics/btx281

Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.

package bioconductor-contibait

(downloads) docker_bioconductor-contibait



depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-dnacopy:


depends bioconductor-exomecopy:


depends bioconductor-genomicalignments:


depends bioconductor-genomicfiles:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-bh:


depends r-clue:

depends r-cluster:

depends r-colorspace:

depends r-data.table:

depends r-diagram:

depends r-ggplot2:

depends r-gplots:

depends r-gtools:

depends r-rcpp:

depends r-reshape2:

depends r-tsp:



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 bioconductor-contibait

and update with::

   mamba update bioconductor-contibait

To create a new environment, run:

mamba create --name myenvname bioconductor-contibait

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 `bioconductor-contibait/tags`_ for valid values for ``<tag>``)

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