ArticleBioinformatics (Oxford, England)2021
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed, 161 citations in OpenAlex.
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- Bayesian Integrative Detection of Structural Variations With False Discovery Rate Control.Biometrical journal. Biometrische Zeitschrift · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
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- Movi 2: Fast and Space-Efficient Queries on Pangenomes.bioRxiv : the preprint server for biology · 2025Article
- LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.Nature communications · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.Research square · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.bioRxiv : the preprint server for biology · 2025Article
- SVHunter: long-read-based structural variation detection through the transformer model.Briefings in bioinformatics · 2025Article
- xRead: a coverage-guided approach for scalable construction of read overlapping graph.GigaScience · 2025Article
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- BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.Bioinformatics advances · 2025Article
- Movi: A fast and cache-efficient full-text pangenome index.iScience · 2024Article
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.Communications biology · 2024Article
- VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.NAR genomics and bioinformatics · 2024Article
- DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering.Briefings in bioinformatics · 2024Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRecent advances in high-throughput long-read sequencers, such as PacBio and Oxford Nanopore sequencers, produce longer reads with more errors than short-read sequencers. In addition to the high error rates of reads, non-uniformity of errors leads to difficulties in various downstream analyses using long reads. Many useful simulators, which characterize long-read error patterns and simulate them, have been developed. However, there is still room for improvement in the simulation of the non-uniformity of errors.
resultsTo capture characteristics of errors in reads for long-read sequencers, here, we introduce a generative model for quality scores, in which a hidden Markov Model with a latest model selection method, called factorized information criteria, is utilized. We evaluated our developed simulator from various points, indicating that our simulator successfully simulates reads that are consistent with real reads. AVAILABILITY AND IMPLEMENTATION: The source codes of PBSIM2 are freely available from https://github.com/yukiteruono/pbsim2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.