Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

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dc.contributor.authorSedlář, Karelcs
dc.contributor.authorKupková, Kristýnacs
dc.contributor.authorProvazník, Ivocs
dc.coverage.issue1cs
dc.coverage.volume15cs
dc.date.accessioned2020-08-04T11:00:16Z
dc.date.available2020-08-04T11:00:16Z
dc.date.issued2016-12-05cs
dc.description.abstractOne of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments. On the other hand, the output of whole metagenomic shotgun sequencing is mixture of short DNA fragments belonging to various genomes, therefore this approach requires more sophisticated computational algorithms for clustering of related sequences, commonly referred to as sequence binning. There are currently two types of binning methods: taxonomy dependent and taxonomy independent. The first type classifies the DNA fragments by performing a standard homology inference against a reference database, while the latter performs the reference-free binning by applying clustering techniques on features extracted from the sequences. In this review, we describe the strategies within the second approach. Although these strategies do not require prior knowledge, they have higher demands on the length of sequences. Besides their basic principle, an overview of particular methods and tools is provided. Furthermore, the review covers the utilization of the methods in context with the length of sequences and discusses the needs for metagenomic data preprocessing in form of initial assembly prior to binning.en
dc.formattextcs
dc.format.extent48-55cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationComputational and Structural Biotechnology Journal. 2016, vol. 15, issue 1, p. 48-55.en
dc.identifier.doi10.1016/j.csbj.2016.11.005cs
dc.identifier.issn2001-0370cs
dc.identifier.other130296cs
dc.identifier.urihttp://hdl.handle.net/11012/69196
dc.language.isoencs
dc.publisherElseviercs
dc.relation.ispartofComputational and Structural Biotechnology Journalcs
dc.relation.urihttp://www.sciencedirect.com/science/article/pii/S2001037016300678cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2001-0370/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectMetagenomicsen
dc.subjectTaxonomy independenten
dc.subjectSequence binningen
dc.subjectGenomic signatureen
dc.subjectAbundanceen
dc.subjectVisualizationen
dc.titleBioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomicsen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-130296en
sync.item.dbtypeVAVen
sync.item.insts2020.08.04 13:00:16en
sync.item.modts2020.08.04 12:46:58en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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