RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes
Joint Authors
Buza, Krisztian
Wilczynski, Bartek
Dojer, Norbert
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-19
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Buza, Krisztian& Wilczynski, Bartek& Dojer, Norbert. 2015. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1066027
Modern Language Association (MLA)
Buza, Krisztian…[et al.]. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes. International Journal of Genomics No. 2015 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1066027
American Medical Association (AMA)
Buza, Krisztian& Wilczynski, Bartek& Dojer, Norbert. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1066027
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066027