Sim3C: simulation of HiC and Meta3C proximity ligation sequencing technologies

DeMaere, Matthew Z.; Darling, Aaron E.

doi:10.1101/134452

2017

DOI: 10.1101/134452

|View full text |Cite

Preprint

Sim3C: simulation of HiC and Meta3C proximity ligation sequencing technologies

Matthew Z. DeMaere

Aaron E. Darling

Abstract: Background

Help me understand this report

View published versions

Search citation statements

Order By: Relevance

Paper Sections

Select...

Citation Types

Supporting

Mentioning

Contrasting

Year Published

2017

Publication Types

Select...

Article1

Relationship

Self Cite0

Independent1

Authors

Journals

Cited by 1 publication

References 40 publications

(76 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies

DeMaere

Darling

2017

GigaScience

View full text Add to dashboard Cite

BackgroundChromosome 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.FindingsWe 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.ConclusionsWe 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.

show abstract

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies

DeMaere

Darling

2017

GigaScience

View full text Add to dashboard Cite

show abstract

scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.

Contact Info

customersupport@researchsolutions.com

10624 S. Eastern Ave., Ste. A-614

Henderson, NV 89052, USA

This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.

Blog Terms and Conditions API Terms Privacy Policy Contact Cookie Preferences Do Not Sell or Share My Personal Information

Made with 💙 for researchers

Part of the Research Solutions Family.

Sim3C: simulation of HiC and Meta3C proximity ligation sequencing technologies

Abstract: Background

Cited by 1 publication

References 40 publications

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies

Contact Info

Product

Resources

About