Non-referenced genome assembly from epigenomic short-read data.

ABSTRACT: Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read d

SUBMITTER: Kaspi A 

PROVIDER: S-EPMC4622496 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature