ArticleBioinformatics (Oxford, England)2018
Simulating the dynamics of targeted capture sequencing with CapSim.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Tracing Species Boundaries Through Genomic Baits: Diagnostic SNP Panels for Genotyping Orchid Pollinaria.Evolutionary applications · 2026Article
- RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.Bioinformatics (Oxford, England) · 2026Article
- Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.Molecular ecology resources · 2022Article
- A broad survey of DNA sequence data simulation tools.Briefings in functional genomics · 2020Review
- A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.Frontiers in genetics · 2019Review
- GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing.BMC bioinformatics · 2018Article
- Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems.Applications in plant sciencesArticle
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Targeted sequencing using capture probes has become increasingly popular in clinical applications due to its scalability and cost-effectiveness. The approach also allows for higher sequencing coverage of the targeted regions resulting in better analysis statistical power. However, because of the dynamics of the hybridization process, it is difficult to evaluate the efficiency of the probe design prior to the experiments which are time consuming and costly. Results: We developed CapSim, a software package for simulation of targeted sequencing. Given a genome sequence and a set of probes, CapSim simulates the fragmentation, the dynamics of probe hybridization and the sequencing of the captured fragments on Illumina and PacBio sequencing platforms. The simulated data can be used for evaluating the performance of the analysis pipeline, as well as the efficiency of the probe design. Parameters of the various stages in the sequencing process can also be evaluated in order to optimize the experiments. Availability and implementation: CapSim is publicly available under BSD license at https://github.com/Devika1/capsim. Contact: l.coin@imb.uq.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.