HYENA
"HYENA" identifies candidate oncogenes activated by enhancer hijacking based on somatic SVs and gene expression data. Click here to download and here to learn more.
SFyNCS
"SFyNCS" detects fusions of both protein-coding genes and non-coding sequences from RNA-Seq data. Click here to download and here to learn more.
Starfish
"Starfish" infers complex SV signatures based on somatic SV and CNV patterns. It can assign individual complex SV event to one of the six signatures identified from PCAWG. Click here to download and here to learn more.
Beehive
"Beehive" is designed to reconstruct tumor evolutionary history based on somatic mutations. The ploidy for each chromosome and tumor purity have to be inferred prior to using this tool. Beehive can also help to validate the inferred purity and ploidy. Click here to download and here to learn more.
Meerkat
"Meerkat" is a computational tool to identify somatic SVs from high-throughput sequencing data. It uses multiple clusters of discordant reads to identify more complex SVs than available methods and uses split-reads to ensure high accuracy, followed by analysis of sequence homology at the breakpoints. The mechanisms forming these SVs can be inferred based on the features of breakpoints. Click here or here to download the software package. Click here to download a demo dataset. Click here to learn more.