DOI: 10.18129/B9.bioc.SimFFPE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SimFFPE.

NGS Read Simulator for FFPE Tissue

Bioconductor version: 3.16

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.

Author: Lanying Wei [aut, cre]

Maintainer: Lanying Wei <lanying.wei at>

Citation (from within R, enter citation("SimFFPE")):


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PDF R Script An introduction to SimFFPE
PDF   Reference Manual
Text   NEWS


biocViews Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License LGPL-3
Depends Biostrings
Imports dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
Suggests BiocStyle
Depends On Me
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