Publication detail

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

SEDLÁŘ, K. KUPKOVÁ, K. PROVAZNÍK, I.

Original Title

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

Type

journal article in Web of Science

Language

English

Original Abstract

One 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.

Keywords

Metagenomics; Taxonomy independent; Sequence binning; Genomic signature; Abundance; Visualization

Authors

SEDLÁŘ, K.; KUPKOVÁ, K.; PROVAZNÍK, I.

Released

5. 12. 2016

Publisher

Elsevier

ISBN

2001-0370

Periodical

Computational and Structural Biotechnology Journal

Year of study

15

Number

1

State

Kingdom of Sweden

Pages from

48

Pages to

55

Pages count

8

URL

http://www.sciencedirect.com/science/article/pii/S2001037016300678

Full text in the Digital Library

http://hdl.handle.net/11012/69196

BibTex

@article{BUT130296,
  author="Karel {Sedlář} and Kristýna {Kupková} and Valentine {Provazník}",
  title="Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics",
  journal="Computational and Structural Biotechnology Journal",
  year="2016",
  volume="15",
  number="1",
  pages="48--55",
  doi="10.1016/j.csbj.2016.11.005",
  issn="2001-0370",
  url="http://www.sciencedirect.com/science/article/pii/S2001037016300678"
}