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Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

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Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

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Bioinformatics [ 1367-4803 ] ; 2015.

RBID : PMC:4896364

Abstract

Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.

Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.

Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG.

Contact:yye@indiana.edu

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896364

DOI: 10.1093/bioinformatics/btv510
PubMed: 26319390
PubMed Central: 4896364

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<author><name sortKey="Ye, Yuzhen" sort="Ye, Yuzhen" uniqKey="Ye Y" first="Yuzhen" last="Ye">Yuzhen Ye</name>
</author>
<author><name sortKey="Tang, Haixu" sort="Tang, Haixu" uniqKey="Tang H" first="Haixu" last="Tang">Haixu Tang</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis</title>
<author><name sortKey="Ye, Yuzhen" sort="Ye, Yuzhen" uniqKey="Ye Y" first="Yuzhen" last="Ye">Yuzhen Ye</name>
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<author><name sortKey="Tang, Haixu" sort="Tang, Haixu" uniqKey="Tang H" first="Haixu" last="Tang">Haixu Tang</name>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
 Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.</p>
<p><bold>Results:</bold>
 Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction <italic>k</italic>
-mers (<italic>k</italic>
-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.</p>
<p><bold>Availability and implementation:</bold>
 TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at <ext-link ext-link-type="uri" xlink:href="http://omics.informatics.indiana.edu/TAG">http://omics.informatics.indiana.edu/TAG</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>yye@indiana.edu</email>
</p>
</div>
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  <front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
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<issn pub-type="epub">1367-4811</issn>
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<article-id pub-id-type="pmc">4896364</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/btv510</article-id>
<article-id pub-id-type="publisher-id">btv510</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Recomb-Seq/Recomb-Cbb</subject>
<subj-group subj-group-type="heading"><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ye</surname>
<given-names>Yuzhen</given-names>
</name>
<xref ref-type="corresp" rid="btv510-COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tang</surname>
<given-names>Haixu</given-names>
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</contrib>
<aff></aff>
</contrib-group>
<author-notes><corresp id="btv510-COR1">*To whom correspondence should be addressed.</corresp>
<fn id="btv510-FN1"><p>Associate Editor: Jan Korbel</p>
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<pub-date pub-type="ppub"><day>01</day>
<month>4</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>29</day>
<month>8</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>29</day>
<month>8</month>
<year>2015</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the 
 							. </pmc-comment>
      <volume>32</volume>
<issue>7</issue>
<fpage>1001</fpage>
<lpage>1008</lpage>
<history><date date-type="received"><day>10</day>
<month>3</month>
<year>2015</year>
</date>
<date date-type="rev-recd"><day>3</day>
<month>6</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>24</day>
<month>8</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2015. Published by Oxford University Press.</copyright-statement>
<copyright-year>2015</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by-nc/4.0/" license-type="creative-commons"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<abstract><p><bold>Motivation:</bold>
 Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.</p>
<p><bold>Results:</bold>
 Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction <italic>k</italic>
-mers (<italic>k</italic>
-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.</p>
<p><bold>Availability and implementation:</bold>
 TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at <ext-link ext-link-type="uri" xlink:href="http://omics.informatics.indiana.edu/TAG">http://omics.informatics.indiana.edu/TAG</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>yye@indiana.edu</email>
</p>
</abstract>
<counts><page-count count="8"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>

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Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

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Abstract

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