Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application.
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....
| Publicado en: | BioMed Research International pp. 1 - 11 |
|---|---|
| Autores principales: | , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
4/11/2019
|
| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=135834791&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 135834791 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 4/11/2019 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 135834791 135834791 135834791 10.1155/2019/7847064 135834791 ppf: 1 ppct: 10 formats: fmt: – @attributes: type: T – @attributes: type: P tig: atl: Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application. aug: au: Kuśmirek, Wiktor Franus, Wiktor Nowak, Robert affil: Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland sug: subj: Algorithms DNA Analysis Sequence Analysis Methods Human Memory Genome Bioinformatics Data Analysis Software ab: 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 of de novo assembly 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. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
|---|