ReviewNature reviews. Genetics2016
A comparison of tools for the simulation of genomic next-generation sequencing data.
Review in Nature reviews. Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 84 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
84 citing papers in PubMed.
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Methods for Investigating the Sperm Epigenome.Advances in experimental medicine and biology · 2026Review
- QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters.Parasites & vectors · 2025Article
- SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data.BMC bioinformatics · 2025Article
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework.Genome biology · 2024Article
- Simulation of nanopore sequencing signal data with tunable parameters.Genome research · 2024Article
- SimHOEPI: A resampling simulator for generating single nucleotide polymorphism data with a high-order epistasis model.Quantitative biology (Beijing, China) · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- Article
- Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- MCSS: microbial community simulator based on structure.Frontiers in microbiology · 2024Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.Genome biology · 2023Article
- Potential persistence mechanisms of the major Anopheles gambiae species complex malaria vectors in sub-Saharan Africa: a narrative review.Malaria journal · 2023Review
- CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads.International journal of molecular sciences · 2023Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.bioRxiv : the preprint server for biology · 2023Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or for gaining an understanding of specific data sets. Several computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand.
Indexed as
Identifiers
What OpenQuestion holds
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.