Table 2. General information about 23 NGS genomic simulators.
| Simulator | Technology | G vs M | Run types | REF | Characterization | Processes | Outputs | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Input | Profile Process | PCR | GV | QS | |||||||||||||
| PA | RE | PR | DF | PA | GU | SW | RE | AL | FO | ||||||||
| 454Sim | 454 | G | SR | x | x | x | x | x | SFF | ||||||||
| ART | 454, ILL, SOL | G | SR, PE, MP | x | x | x | x | x | x | x | x | x | x | SFF/FQ | |||
| ArtificialFastqGenerator | ILL | G | PE | x | x | x | x | x | x | FQ | |||||||
| BEAR | 454, ILL, ITO | G,M | SR, PE | x | x | x | x | x | x | FQ | |||||||
| CuReSim | 454, ILL, SOL, ITO | G | SR | x | x | x | x | FQ | |||||||||
| DWGSIM (dnaa) | ILL, SOL, ITO | G | SR, PE, MP | x | x | x | x | x | x | x | FQ | ||||||
| EAGLE | 454, ILL, PCB, ITO | G | SR, PE | x | x | x | x | x | x | x | FQ | ||||||
| FASTQSim | ILL, SOL, PCB, ITO | G,M | SR | x | x | x | x | x | x | x | FQ | ||||||
| Flowsim | 454 | G | SR, PE | x | x | x | x | x | x | x | x | SFF | |||||
| GemSim | 454, ILL | G,M | SR, PE | x | x | x | x | x | x | x | FQ | ||||||
| Grinder | 454, ILL, SNG | G,M | SR, PE, MP | x | x | x | x | x | x | x | x | FQ | |||||
| Mason | 454, ILL, SNG | G | SR, PE, MP | x | x | x | x | x | x | x | x | FA/FQ | |||||
| MetaSim | 454,ILL, SNG | G,M | SR, PE, MP | x | x | x | x | FA | |||||||||
| NeSSM | 454, ILL | M | SR, PE | x | x | x | x | x | x | FQ | |||||||
| pbsim | PCB | G | CLR/CCS | x | x | x | x | x | x | FQ | |||||||
| pIRS | ILL | G,M | PE | x | x | x | x | x | x | x | x | FQ | |||||
| ReadSim | PCB, ONT | G | SR | x | x | x | x | x | x | FQ | |||||||
| simhtsd | 454, ILL | G | SR, PE | x | x | x | x | FQ | |||||||||
| simNGS | ILL | G | SR, PE | x | x | x | x | x | x | FQ | |||||||
| SimSeq | ILL | G | SR, PE, MP | x | x | x | x | x | x | x | x | SAM/BAM | |||||
| SInC | ILL | G | PE | x | x | x | x | x | x | x | FQ | ||||||
| wgsim | ILL, SOL | G | SR | x | x | x | x | x | x | FQ | |||||||
| xs | 454, ILL, SOL, ITO | G | SR,PE | x | x | x | x | FQ | |||||||||
454: Roche’s 454. ILL: Illumina. SOL: SOLiD. ITO: Ion Torrent. PCB: Pacific Biosciences. ONT: Oxford Nanopore Technologies. SNG: Sanger. G: Genomics. M: Metagenomics. PA: Parameters. RE: Reads. PR: Profile. DF: Default Profile. GU: Guide to generate profiles. SW: Specific software to generate profile. PCR: Polymerase Chain Reaction. GV: Genomic variants. QS: Quality scores. FO: Format. AL: Alignments. FA: Fasta. FQ: Fastq. SFF: Standard Flowgram Format. SAM Sequence Alignment Map. BAM: Compressed SAM File. Also accessible in http://darwin.uvigo.es/ngs-simulators/