ReviewBriefings in functional genomics2020
A broad survey of DNA sequence data simulation tools.
Review in Briefings in functional genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences.NAR genomics and bioinformatics · 2026Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- MCSS: microbial community simulator based on structure.Frontiers in microbiology · 2024Article
- PBSIM3: a simulator for all types of PacBio and ONT long reads.NAR genomics and bioinformatics · 2022Article
- J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.BMC bioinformatics · 2022Article
- Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.Environmental microbiome · 2022Article
- Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan.PLoS computational biology · 2021Article
- Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches.Briefings in bioinformatics · 2021Article
- PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores.Bioinformatics (Oxford, England) · 2021Article
- ReSeq simulates realistic Illumina high-throughput sequencing data.Genome biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. We provide a succinct description of each tool and suggest which tool is most appropriate for the given different scenarios. Given the multitude of similar yet non-identical tools, researchers can use this review as a guide to inform their choice of DNA sequence simulation tool. This paves the way towards assessing existing tools in a unified framework, as well as enabling different simulation scenario analysis within the same framework.
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.