PacBio sequencing simulator Long Description (required)
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. https://github.com/NWPU-903PR/NPBSS_Octave
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 29788930 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=29788930, Primary Citation
[Pubmed ID: 32976553 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=32976553, , Application
[Pubmed ID: 35668508 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35668508, , Application