recipe bioconductor-simffpe

NGS Read Simulator for FFPE Tissue






The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.

package bioconductor-simffpe

(downloads) docker_bioconductor-simffpe



depends bioconductor-biostrings:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rsamtools:


depends r-base:


depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-truncnorm:



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-simffpe

and update with::

   mamba update bioconductor-simffpe

To create a new environment, run:

mamba create --name myenvname bioconductor-simffpe

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

Download stats