Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Identifieur interne : 001518 ( Main/Exploration ); précédent : 001517; suivant : 001519Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Auteurs : Yuzhen Ye ; Haixu TangSource :
- Bioinformatics [ 1367-4803 ] ; 2015.
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DOI: 10.1093/bioinformatics/btv510
PubMed: 26319390
PubMed Central: 4896364
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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></author><author><name sortKey="Tang, Haixu" sort="Tang, Haixu" uniqKey="Tang H" first="Haixu" last="Tang">Haixu Tang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26319390</idno><idno type="pmc">4896364</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896364</idno><idno type="RBID">PMC:4896364</idno><idno type="doi">10.1093/bioinformatics/btv510</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000084</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000084</idno><idno type="wicri:Area/Pmc/Curation">000084</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000084</idno><idno type="wicri:Area/Pmc/Checkpoint">000C91</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000C91</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:26319390</idno><idno type="wicri:Area/PubMed/Corpus">001484</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001484</idno><idno type="wicri:Area/PubMed/Curation">001484</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001484</idno><idno type="wicri:Area/PubMed/Checkpoint">000E55</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000E55</idno><idno type="wicri:Area/Ncbi/Merge">001254</idno><idno type="wicri:Area/Ncbi/Curation">001254</idno><idno type="wicri:Area/Ncbi/Checkpoint">001254</idno><idno type="wicri:doubleKey">1367-4803:2015:Ye Y:utilizing:de:bruijn</idno><idno type="wicri:Area/Main/Merge">001523</idno><idno type="wicri:Area/Main/Curation">001518</idno><idno type="wicri:Area/Main/Exploration">001518</idno></publicationStmt><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></author><author><name sortKey="Tang, Haixu" sort="Tang, Haixu" uniqKey="Tang H" first="Haixu" last="Tang">Haixu Tang</name></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1367-4811</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Metagenome</term><term>Metagenomics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Métagénome</term><term>Métagénomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Metagenome</term><term>Metagenomics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Métagénome</term><term>Métagénomique</term></keywords></textClass></profileDesc></teiHeader><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></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S. 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