FilterFFPE - FFPE Artificial Chimeric Read Filter for NGS data
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
Last updated 4 months ago
structuralvariationsequencingalignmentqualitycontrolpreprocessing
0.49 score 34 dependenciesSimFFPE - 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.
Last updated 4 months ago
sequencingalignmentmultiplecomparisonsequencematchingdataimport
0.49 score 50 dependencies