Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application

Wiktor Kuśmirek , W. Franus , Robert Marek Nowak

Abstract

Currently, third-generation sequencing techniques, which make it possible to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities for combining data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, the result ofde novoassembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of an appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions. Our implementation is found to outperform other state-of-the-art tools in terms of speed and memory requirements, which may enable its usage for organisms with a large genome, something which is not possible in existing applications. The presented application has many advantages: (i) it significantly optimizes memory and reduces computation time; (ii) it fills gaps with an appropriate fragment of a specified long DNA read; (iii) it reduces the number of spanned and unspanned gaps in existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, Docker image, and source code can be downloaded from project homepage.
Author Wiktor Kuśmirek (FEIT / IN)
Wiktor Kuśmirek,,
- The Institute of Computer Science
, W. Franus - [Politechnika Warszawska]
W. Franus,,
-
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, Robert Marek Nowak (FEIT / IN)
Robert Marek Nowak,,
- The Institute of Computer Science
Journal seriesBioMed Research International [Journal of Biomedicine and Biotechnology], ISSN 1110-7243, [1110-7251, 2314-6133, 2314-6141], (A 25 pkt, Not active)
Issue year2019
Vol2019
Pages1-10
Publication size in sheets0.5
ASJC Classification2400 General Immunology and Microbiology; 1300 General Biochemistry, Genetics and Molecular Biology; 2700 General Medicine; 2307 Health, Toxicology and Mutagenesis; 1311 Genetics; 1312 Molecular Biology; 1313 Molecular Medicine; 1305 Biotechnology
DOIDOI:10.1155/2019/7847064
URL https://www.hindawi.com/journals/bmri/2019/7847064/
Languageen angielski
File
7847064.pdf 620.15 KB
Score (nominal)25
ScoreMinisterial score = 25.0, 23-07-2019, ArticleFromJournal
Publication indicators Scopus Citations = 0; WoS Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.875; WoS Impact Factor: 2017 = 2.583 (2) - 2017=2.931 (5)
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