Title: Linking de novo assembly results with long DNA reads by dnaasm-link application,
Abstract: Currently, third-generation sequencing techniques, which allow to obtain much
longer DNA reads compared to the next-generation sequencing technologies, are
becoming more and more popular. There are many possibilities to combine data
from next-generation and third-generation sequencing.
Herein, we present a new application called dnaasm-link for linking contigs,
a result of \textit{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 appropriate long DNA read, which improves the consistency
of the resulting DNA sequences. This feature is very important, in particular
for complex DNA regions, as presented in the paper. Finally, our implementation
outperforms other state-of-the-art tools in terms of speed and memory
requirements, which may enable the usage of the presented application for
organisms with a large genome, which is not possible in~existing applications.
The presented application has many advantages as (i) significant memory
optimization and reduction of computation time (ii) filling the gaps through
the appropriate fragment of a specified long DNA read (iii) reducing number of
spanned and unspanned gaps in the 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 are available at this http URL.