23,730 research outputs found
Linking de novo assembly results with long DNA reads by dnaasm-link application
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 http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure
Cerulean: A hybrid assembly using high throughput short and long reads
Genome assembly using high throughput data with short reads, arguably,
remains an unresolvable task in repetitive genomes, since when the length of a
repeat exceeds the read length, it becomes difficult to unambiguously connect
the flanking regions. The emergence of third generation sequencing (Pacific
Biosciences) with long reads enables the opportunity to resolve complicated
repeats that could not be resolved by the short read data. However, these long
reads have high error rate and it is an uphill task to assemble the genome
without using additional high quality short reads. Recently, Koren et al. 2012
proposed an approach to use high quality short reads data to correct these long
reads and, thus, make the assembly from long reads possible. However, due to
the large size of both dataset (short and long reads), error-correction of
these long reads requires excessively high computational resources, even on
small bacterial genomes. In this work, instead of error correction of long
reads, we first assemble the short reads and later map these long reads on the
assembly graph to resolve repeats.
Contribution: We present a hybrid assembly approach that is both
computationally effective and produces high quality assemblies. Our algorithm
first operates with a simplified version of the assembly graph consisting only
of long contigs and gradually improves the assembly by adding smaller contigs
in each iteration. In contrast to the state-of-the-art long reads error
correction technique, which requires high computational resources and long
running time on a supercomputer even for bacterial genome datasets, our
software can produce comparable assembly using only a standard desktop in a
short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction
In this article, we present QuASeR, a reference-free DNA sequence
reconstruction implementation via de novo assembly on both gate-based and
quantum annealing platforms. Each one of the four steps of the implementation
(TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept
examples to target both the genomics research community and quantum application
developers in a self-contained manner. The details of the implementation are
discussed for the various layers of the quantum full-stack accelerator design.
We also highlight the limitations of current classical simulation and available
quantum hardware systems. The implementation is open-source and can be found on
https://github.com/prince-ph0en1x/QuASeR.Comment: 24 page
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Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.
The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia
Jabba: hybrid error correction for long sequencing reads using maximal exact matches
Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is that this mapping is constructed with a seed and extend methodology, using maximal exact matches as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of maximal exact matches in the context of third generation reads are presented
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