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SimFFPE

Bioc current

NGS Read Simulator for FFPE Tissue

v1.24.0 · software · LGPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.11 · Apr 28, 2020

Current · Requires R 4.6

1.0 In 13 of 49 releases 3.23

Description

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.

Code

Code metrics have not been computed for this package yet.

Topics

Software › Technology › Sequencing
Software › WorkflowStep › Alignment
Software › WorkflowStep › MultipleComparison
Software › BiologicalQuestion › SequenceMatching
Software › Infrastructure › DataImport

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