GSR: Simulator - NPBSS

Basic Package Attributes
AttributeValue
Title 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.
Version 1.0.0
Project Started 2018
Last Release 3 years, 6 months ago
Homepagehttps://github.com/NWPU-903PR/NPBSS_Octave
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 verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataSequencing Reads,
Variations
Simulation MethodResample Existing Data,
Input
Data Type
File format
Output
Data Type
Sequencing ReadsPacBio,
File FormatFasta or Fastq,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows,
LanguageOther,
License
GSR Certification

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