- 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¶
- 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:
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
myenvnamebeing 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/bioconductor-simffpe:<tag> (see `bioconductor-simffpe/tags`_ for valid values for ``<tag>``)