| AMOS | A fast and flexible API for genome assembly and manipulations |
| Assemblytics | Interactive analysis of variants within an assembly |
| Celera Assembler | The program used to assemble the human genome at Celera Genomics in 2001 |
| CloudBurst | Highly Sensitive Short Read Mapping with MapReduce |
| Contrail | Assembly of Large Genomes using Cloud Computing |
| Crossbow | Whole Genome Resequencing Analysis in the Clouds |
| CrossStitch | Hybrid Phasing and Personal Genome Construction |
| FALCON | Phased Diploid Genome Assembly with PacBio sequencing reads |
| Genome-indexing | Rapid Burrows-Wheeler Transform Construction with MapReduce |
| GenomeScope | Estimate genomic properties from unassembled sequencing reads |
| Ginkgo | Interactive analysis and assessment of single-cell copy-number variations |
| Hawkeye | Genome Assembly Viewer and Analysis Tool. |
| LRSim | Linked Read Simulator |
| MUMmer | A modular system for the rapid whole genome alignment of finished or draft sequence |
| MUMmerGPU | High-throughput Sequence Alignment on the GPU using CUDA GPGPU API from nVidia |
| NanoCorr | Hybrid Error Correction of Oxford Nanopore Sequencing Reads |
| NGM-LR | Fast and Accurate Mapping of Long Reads |
| PhyloTrac | Visualization and Analysis tool for the PhlyoChip |
| Quake | Quality guided correction and filtration of errors in short reads. |
| Ribbon | Visualization of Long Read Alignments |
| Scalpel | Indel variant analysis of short-read sequencing data |
| SplitMem | Pan Genome Analysis with suffix skips |
| Sniffles | Detection of Structural Variations from Long Reads |
| SURVIVOR | Detection and Analysis of Structural Variations |
| Teaser | Fast personalized benchmarks and optimization for NGS read mapping |
