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Non-referenced genome assembly from epigenomic short-read data

Version 2 2024-06-03, 07:12
Version 1 2015-02-26, 11:47
journal contribution
posted on 2024-06-03, 07:12 authored by A Kaspi, Mark ZiemannMark Ziemann, ST Keating, I Khurana, Timothy ConnorTimothy Connor, Briana RandallBriana Randall, A Cooper, R Lazarus, Ken WalderKen Walder, P Zimmet, A El-Osta
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.

History

Journal

Epigenetics

Volume

9

Pagination

1329-1338

Location

United States

ISSN

1559-2294

eISSN

1559-2308

Language

English

Publication classification

C Journal article, C1 Refereed article in a scholarly journal

Copyright notice

2014, Taylor & Francis

Issue

10

Publisher

TAYLOR & FRANCIS INC