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International Journal of Genomics
Volume 2015 (2015), Article ID 563482, 10 pages
Research Article

RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes

Faculty of Mathematics, Informatics and Mechanics (MIM), University of Warsaw, Banacha 2, 02-097 Warsaw, Poland

Received 18 March 2015; Revised 27 May 2015; Accepted 31 May 2015

Academic Editor: Chun-Yuan Lin

Copyright © 2015 Krisztian Buza et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.