e-RGA: enhanced Reference Guided Assembly of Complex Genomes

Authors

  • Francesco Vezzi DIMI department of Informatics and Mathematics University of Udine, Udine, Italy IGA institute of applied genomics, Udine, Italy
  • Federica Cattonaro IGA institute of applied genomics, Udine, Italy
  • Alberto Policriti DIMI department of Informatics and Mathematics University of Udine, Udine, Italy IGA institute of applied genomics, Udine, Italy

DOI:

https://doi.org/10.14806/ej.17.1.208

Keywords:

de novo assembly, reference guided assembly, next generation sequencing

Abstract

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tools able to assemble, de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced results.
Embnet.journal 17.1

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Published

2011-08-02

Issue

Vol. 17 No. 1: Next Generation Sequencing Data Analysis

Section

Research Papers

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