| BioBricks | Software to simulate recombination to assess ancestry blocks |
| FALCON | Phased Diploid Genome Assembly with PacBio sequencing reads |
| GenomeScope | Estimate genomic properties from unassembled sequencing reads |
| LRSim | Linked Read Simulator |
| MuMmer SGE | Parallization script for MUMMer. |
| NGM | Short read mapper especially suitable for high SNP rates |
| NGM-LR | Fast and Accurate Mapping of Long Reads |
| Paragraph | Genome graph based SV genotyping |
| PhaseME | Phasing QC and utilization of linkage data |
| Princess | Software for haplotype resolved detection of SNV, SV and methylation |
| Read2Tree | Software for mapping reads directly onto orthology groups |
| Sniffles | Detection of Structural Variations from Long Reads |
| SURVIVOR | Detection and Analysis of Structural Variations |
| SVCollector | Method to optimally select samples for validation and resequencing based on a multi sample VCF. |
| SVHound | Statistical software to predict SV in a cohort that have not been found yet. |
| Teaser | Fast personalized benchmarks and optimization for NGS read mapping |
| Vulcan | Utilizing two scoring functions to improve long read mapping |