ArticleGigaScience2017
NanoSim: nanopore sequence read simulator based on statistical characterization.
Article in GigaScience, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed.
- Transgenerational chromosome repair in the asexual bdelloid rotiferScience advances · 2026Article
- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
- Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.Bioinformatics (Oxford, England) · 2026Article
- RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.Bioinformatics (Oxford, England) · 2026Article
- Genestrip: exact and efficient read classification for selected groups of organisms.BMC bioinformatics · 2026Article
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.PLoS computational biology · 2026Article
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- ntStat: k-mer characterization using occurrence statistics in raw sequencing data.PLoS computational biology · 2026Article
- MIrROR release 02: Expanded and refined 16S-ITS-23S rRNA operon dataset.Scientific data · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Context-aware simulation enables systematic optimization of long-read mapping parameters.GigaScience · 2026Article
- Article
- TNRSim - a simulator of truncated oxford nanopore direct RNA long reads for isoform analysis.Frontiers in bioinformatics · 2026Article
- RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.bioRxiv : the preprint server for biology · 2025Article
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
82 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, the output of which could be used to benchmark analysis tools. Results: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim. Conclusion: In this work, we model the base-calling errors of ONT reads to inform the simulation of sequences with similar characteristics. We showcase the performance of NanoSim on publicly available datasets generated using the R7 and R7.3 chemistries and different sequencing kits and compare the resulting synthetic reads to those of other long-sequence simulators and experimental ONT reads. We expect NanoSim to have an enabling role in the field and benefit the development of scalable next-generation sequencing technologies for the long nanopore reads, including genome assembly, mutation detection, and even metagenomic analysis software.
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Registered trials
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.