Table 1 Popular in silico read simulators
From: FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets
Technology | Supported platforms | Capabilities | Limitations |
|---|---|---|---|
PBSim [9] | PacBio | Simulates both continuous long reads (CLRs) and circular | Limited insertion and deletion (indel) |
| Â | Â | consensus sequences (CCS); supports sampling-based | support |
| Â | Â | simulation (in which both length and quality scores are | Â |
| Â | Â | sampled from a real read set) and model-based simulation | Â |
FlowSim [8] | Roche 454 | Simulates read length and quality in flow space | No indel support |
dwgsim [10] | Illumina, IonTorrent | Whole-genome simulator | Uniform read length |
ART [11] | Roche 454, Illumina Solexa | Read error model, quality profiles | No simulation of indels for short |
| Â | Â | Â | tandem repeats (STRs) |
Maq [12] | Illumina Solexa | Single nucleotide polymorphism (SNP) simulation | Fixed mutation rate does not model |
| Â | Â | Â | real-world data |
Grinder [13] | Platform-independent | Shotgun or amplicon read libraries | Limited indel support |
MetaSim [14] | 454, Illumina, Sanger | Simulation, assembly, mapping | Does not assign quality values to reads |
GemSim [15] | 454, Illumina | Simulation | Fixed length and mutation rates |