recipe bismark

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.



GPL3 / GNU General Public License v3 (GPLv3)




biotools: bismark, usegalaxy-eu: bismark_bowtie2

package bismark

(downloads) docker_bismark



depends bowtie2:

depends coreutils:

depends hisat2:

depends minimap2:

depends perl:

depends samtools:



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 bismark

and update with::

   mamba update bismark

To create a new environment, run:

mamba create --name myenvname bismark

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 `bismark/tags`_ for valid values for ``<tag>``)

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