ArticleBMC bioinformatics2018
NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Comparison of the microbiome of sputum from HIV/AIDS patients using PacBio 16S rRNA sequencing and ddPCR.BMC infectious diseases · 2025Article
- Effects of antibiotics on chicken gut microbiota: community alterations and pathogen identification.Frontiers in microbiology · 2025Article
- The Research Progress of Single-Molecule Sequencing and Its Significance in Nucleic Acid Metrology.Biosensors · 2024Review
- The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease.Archives of microbiology · 2024Article
- pathMap: a path-based mapping tool for long noisy reads with high sensitivity.Briefings in bioinformatics · 2024Article
- Cutting edge tools in the field of soil microbiology.Current research in microbial sciences · 2024Review
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.Genome biology · 2023Article
- invMap: a sensitive mapping tool for long noisy reads with inversion structural variants.Bioinformatics (Oxford, England) · 2023Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.bioRxiv : the preprint server for biology · 2023Article
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- Article
- Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment.Parasites & vectors · 2022Article
- kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on theFrontiers in genetics · 2022Article
- Deciphering the Molecular Basis for Attenuation ofVaccines · 2021Article
- PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores.Bioinformatics (Oxford, England) · 2021Article
- Finding long tandem repeats in long noisy reads.Bioinformatics (Oxford, England) · 2021Article
- Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.Frontiers in microbiology · 2021Article
- rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites.BioMed research international · 2021Article
- Twelve quick steps for genome assembly and annotation in the classroom.PLoS computational biology · 2020Article
- smsMap: mapping single molecule sequencing reads by locating the alignment starting positions.BMC bioinformatics · 2020Article
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2 authors.
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Abstract
backgroundPacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of subsequent analysis tools. Although there are several available simulators (e.g., PBSIM, SimLoRD and FASTQSim) that target the specific generation of PacBio libraries, the error rate of simulated sequences is not well matched to the quality value of raw PacBio datasets, especially for PacBio's continuous long reads (CLR).
resultsBy 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.
conclusionNPBSS simulator is convenient to use with efficient computation and flexible parameters setting. Its generating PacBio CLR reads are more like real PacBio datasets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.