SimFFPE

NGS Read Simulator for FFPE Tissue

Bioconductor version: 3.24 · Package version: 1.25.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SimFFPE")