Infrastructure
Variant DETECTION
Bassovac
Improved Bayesian inversion somatic caller [presentation] [github]
BreakDancer
SV caller using paired-end sequence data [video] [publication] [github]
CMDS
Recurrent CNV caller using population data [publication] [github]
MSIsensor
Microsatellite instability detection using paired tumor-normal [publication] [github]
PASSion
Paired-end RNA-Seq splice site detection [publication] [github]
Pindel-c
Indel caller using pattern growth [publication] [publication] [github]
SomaticSniper
Bayesian somatic SNV caller [video] [publication] [github]
SquareDancer
Split reads for SV discovery [video] [github]
TIGRA_SV
De novo assembly of SV breakpoints [publication] [download]
VarScan
Germline and somatic SNV and CNV caller [publication] [github]
VirusScan
Detect virus from next generation sequencing data [publication] [github]
Interpretation
HotSpot3D
3D hotspot mutation proximity analysis tool [publication] [github]
MuSiC
A suite of variant interpretation tools [publication] [website]
PathScan
Pathway analysis tool using population data [publication]
SciClone
Infer subclonal architecture of tumors [publication] [github]
Visualization
Breakpoint Surveyor
A comprehensive pipeline to analyze and visualize structural variants [publication] [github]
Lolliplot
A mutation distribution graphics tool
Pairoscope
SV visualization tool [github]