GSR: Simulator - NPBSS
Attribute | Value |
---|---|
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 | 6 years ago |
Homepage | https://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 | Accessibility |
Last evaluated | 09-30-2021 (904 days ago) |
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. |
Attribute Category | Attribute |
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Target | |
Type of Simulated Data | Sequencing Reads, |
Variations | |
Simulation Method | Resample Existing Data, |
Input | |
Data Type | |
File format | |
Output | |
Data Type | |
Sequencing Reads | PacBio, |
File Format | Fasta 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 | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, |
Language | Other, |
License | |
GSR Certification | Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used NPBSS.
2022
Hickson J, Athayde LFA, Miranda TG, Junior PAS, Dos Santos AC, da Cunha Galvão LM, da Câmara ACJ, Bartholomeu DC, de Souza RCM, Murta SMF, et al., Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment., Parasit Vectors, 06-06-2022 [Abstract]
2021
Ono Y, Asai K, Hamada M, PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores., Bioinformatics, 05-05-2021 [Abstract]