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

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 ligatio

SUBMITTER: DeMaere MZ 

PROVIDER: S-EPMC5827349 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature