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

Antony Kaspi, Mark Ziemann, Samuel T Keating, Ishant Khurana, Timothy Connor, Briana Spolding, Adrian Cooper, Ross Lazarus, Ken Walder, Paul Zimmet, Assam El-Osta

Index: Epigenetics 9(10) , 1329-38, (2014)

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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 data.