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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)
   consensus sequences (CCS); supports sampling-based support
   simulation (in which both length and quality scores are  
   sampled from a real read set) and model-based simulation  
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
    tandem repeats (STRs)
Maq [12] Illumina Solexa Single nucleotide polymorphism (SNP) simulation Fixed mutation rate does not model
    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