GSR: Simulator - NPBSS
|Short Description||PacBio sequencing simulator|
|Long Description||By analyzing the characteristic features of CLR data from PacBio SMRT (single molecule real time) sequencing, we developed a new PacBio sequencing simulator (called NPBSS) for producing CLR reads. NPBSS simulator firstly samples the read sequences according to the read length logarithmic normal distribution, and choses different base quality values with different proportions. Then, NPBSS computes the overall error probability of each base in the read sequence with an empirical model, and calculates the deletion, substitution and insertion probabilities with the overall error probability to generate the PacBio CLR reads. Alignment results demonstrate that NPBSS fits the error rate of the PacBio CLR reads better than PBSIM and FASTQSim. In addition, the assembly results also show that simulated sequences of NPBSS are more like real PacBio CLR data.|
|Last Release||3 years, 6 months ago|
|Citations||Wei ZG, Zhang SW, NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model., BMC Bioinformatics, 05-22-2018 [ Abstract, cited in PMC ]|
|GSR Certification||This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.|
|Author verification||The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.|
|Type of Simulated Data||Sequencing Reads,|
|Simulation Method||Resample Existing Data,|
|File Format||Fasta or Fastq,|
|Population Size Changes|
No example publication using NPBSS has been provided.
Please propose new citations if you are aware of publications that use this software.