ArticleGigaScience2018
Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.Genome biology · 2025Article
- Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.NAR genomics and bioinformatics · 2025Article
- Hidden origami inmBio · 2025Article
- Accelerating 3D genomics data analysis with Microcket.Communications biology · 2024Article
- Article
- Tracing cancer evolution and heterogeneity using Hi-C.Nature communications · 2023Article
- SpecHLA enables full-resolution HLA typing from sequencing data.Cell reports methods · 2023Article
- GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C.Genome biology · 2023Article
- Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts.Microbial genomics · 2023Article
- scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.Journal of molecular cell biology · 2023Article
- Locus-specific chromatin profiling of evolutionarily young transposable elements.Nucleic acids research · 2022Article
- Lysis-Hi-C as a method to study polymicrobial communities and eDNA.Molecular ecology resources · 2022Article
- Article
- qc3C: Reference-free quality control for Hi-C sequencing data.PLoS computational biology · 2021Article
- Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.Frontiers in microbiology · 2021Article
- Benchmark of software tools for prokaryotic chromosomal interaction domain identification.Bioinformatics (Oxford, England) · 2020Article
- Twelve quick steps for genome assembly and annotation in the classroom.PLoS computational biology · 2020Article
- FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation.Nature methods · 2020Article
- Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types.Epigenetics & chromatin · 2019Article
- Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes inMicroorganisms · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. Conclusions: We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respect to experimental hypothesis testing.
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.