In silico read normalization using set multi-cover optimization
Identifieur interne : 000A98 ( Main/Exploration ); précédent : 000A97; suivant : 000A99In silico read normalization using set multi-cover optimization
Auteurs : Dilip A. Durai [Allemagne] ; Marcel H. Schulz [Allemagne]Source :
- Bioinformatics [ 1367-4803 ] ; 2018.
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Abstract
De Bruijn graphs are a common assembly data structure for sequencing datasets. But with the advances in sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, which removes redundancy in datasets, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve important
Here, normalization is phrased as a
ORNA is available at
Url:
DOI: 10.1093/bioinformatics/bty307
PubMed: 29912280
PubMed Central: 6157080
Affiliations:
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Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic>
read normalization using set multi-cover optimization</title>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Computational Biology</term>
<term>Computer Simulation</term>
<term>Sequence Analysis, RNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ARN</term>
<term>Biologie informatique</term>
<term>Simulation numérique</term>
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<term>Computational Biology</term>
<term>Computer Simulation</term>
<term>Sequence Analysis, RNA</term>
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<term>Analyse de séquence d'ARN</term>
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<front><div type="abstract" xml:lang="en"><title>Abstract</title>
<sec id="s1"><title>Motivation</title>
<p>De Bruijn graphs are a common assembly data structure for sequencing datasets. But with the advances in sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, which removes redundancy in datasets, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve important <italic>k</italic>
-mers that form connections between regions in the graph.</p>
</sec>
<sec id="s2"><title>Results</title>
<p>Here, normalization is phrased as a <italic>set multi-cover problem</italic>
on reads and a heuristic algorithm, Optimized Read Normalization Algorithm (ORNA), is proposed. ORNA normalizes to the minimum number of reads required to retain all <italic>k</italic>
-mers and their relative <italic>k</italic>
-mer abundances from the original dataset. Hence, all connections from the original graph are preserved. ORNA was tested on various RNA-seq datasets with different coverage values. It was compared to the current normalization algorithms and was found to be performing better. Normalizing error corrected data allows for more accurate assemblies compared to the normalized uncorrected dataset. Further, an application is proposed in which multiple datasets are combined and normalized to predict novel transcripts that would have been missed otherwise. Finally, ORNA is a general purpose normalization algorithm that is fast and significantly reduces datasets with loss of assembly quality in between [1, 30]% depending on reduction stringency.</p>
</sec>
<sec id="s3"><title>Availability and implementation</title>
<p>ORNA is available at <ext-link ext-link-type="uri" xlink:href="https://github.com/SchulzLab/ORNA">https://github.com/SchulzLab/ORNA</ext-link>
.</p>
</sec>
<sec id="s4"><title>Supplementary information</title>
<p><xref ref-type="supplementary-material" rid="sup1">Supplementary data</xref>
are available at <italic>Bioinformatics</italic>
online.</p>
</sec>
</div>
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