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Abstract Background Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. Results According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes. Generally, current tools have used the normalized frequency of k-tuples directly, but this represents an absolute, not relative, sequence composition. Therefore, we attempted to model contigs using relative k-tuple composition, followed by measuring dissimilarity between contigs using d 2 S $$ {d}_2^S $$ . The d 2 S $$ {d}_2^S $$ was designed to measure the dissimilarity between two long sequences or Next-Generation Sequencing data with the Markov models of the background genomes. This method was effective in revealing group and gradient relationships between genomes, metagenomes and metatranscriptomes. With many binning tools available, we do not try to bin contigs from scratch. Instead, we developed d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ to adjust contigs among bins based on the output of existing binning tools for a single metagenomic sample. The tool is taxonomy-free and depends only on k-tuples. To evaluate the performance of d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ , five widely used binning tools with different strategies of sequence composition or the hybrid of sequence composition and abundance were selected to bin six synthetic and real datasets, after which d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ was applied to adjust the binning results. Our experiments showed that d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ consistently achieves the best performance with tuple length k = 6 under the independent identically distributed (i.i.d.) background model. Using the metrics of recall, precision and ARI (Adjusted Rand Index), d 2 S B i n $$ {d}_2^S\mathrm{Bin} $$ improves the binning performance in 28 out of 30 testing experiments (6 datasets with 5 binning tools). The d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ is available at https://github.com/kunWangkun/d2SBin . Conclusions Experiments showed that d 2 S $$ {d}_2^S $$ accurately measures the dissimilarity between contigs of metagenomic reads and that relative sequence composition is more reasonable to bin the contigs. The d 2 S Bin $$ {d}_2^S\mathrm{Bin} $$ can be applied to any existing contig-binning tools for single metagenomic samples to obtain better binning results.

BMC bioinformatics, 2017-09, Vol.18 (1), p.1-14

Improving contig binning of metagenomic data using d 2 S $$ {d}_2^S $$ oligonucleotide frequency dissimilarity

Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes. Generally, current tools have used the normalized frequency of k-tuples directly, but this represents an absolute, not relative, sequence composition. Therefore, we attempted to model contigs using relative k-tuple composition, followed by measuring dissimilarity between contigs using d2S\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{document}. The d2S\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{document} was designed to measure the dissimilarity between two long sequences or Next-Generation Sequencing data with the Markov models of the background genomes. This method was effective in revealing group and gradient relationships between genomes, metagenomes and metatranscriptomes. With many binning tools available, we do not try to bin contigs from scratch. Instead, we developed d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} to adjust contigs among bins based on the output of existing binning tools for a single metagenomic sample. The tool is taxonomy-free and depends only on k-tuples. To evaluate the performance of d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document}, five widely used binning tools with different strategies of sequence composition or the hybrid of sequence composition and abundance were selected to bin six synthetic and real datasets, after which d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} was applied to adjust the binning results. Our experiments showed that d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} consistently achieves the best performance with tuple length k = 6 under the independent identically distributed (i.i.d.) background model. Using the metrics of recall, precision and ARI (Adjusted Rand Index), d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} improves the binning performance in 28 out of 30 testing experiments (6 datasets with 5 binning tools). The d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} is available at https://github.com/kunWangkun/d2SBin. Experiments showed that d2S\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{document} accurately measures the dissimilarity between contigs of metagenomic reads and that relative sequence composition is more reasonable to bin the contigs. The d2SBin\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S\mathrm{Bin} $$\end{document} can be applied to any existing contig-binning tools for single metagenomic samples to obtain better binning results.

BMC bioinformatics, 2017-09, Vol.18 (1)

Improving contig binning of metagenomic data using d2S\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{document} oligonucleotide frequency dissimilarity

Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development.
According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes. Generally, current tools have used the normalized frequency of k-tuples directly, but this represents an absolute, not relative, sequence composition. Therefore, we attempted to model contigs using relative k-tuple composition, followed by measuring dissimilarity between contigs using [Formula: see text]. The [Formula: see text] was designed to measure the dissimilarity between two long sequences or Next-Generation Sequencing data with the Markov models of the background genomes. This method was effective in revealing group and gradient relationships between genomes, metagenomes and metatranscriptomes. With many binning tools available, we do not try to bin contigs from scratch. Instead, we developed [Formula: see text] to adjust contigs among bins based on the output of existing binning tools for a single metagenomic sample. The tool is taxonomy-free and depends only on k-tuples. To evaluate the performance of [Formula: see text], five widely used binning tools with different strategies of sequence composition or the hybrid of sequence composition and abundance were selected to bin six synthetic and real datasets, after which [Formula: see text] was applied to adjust the binning results. Our experiments showed that [Formula: see text] consistently achieves the best performance with tuple length k = 6 under the independent identically distributed (i.i.d.) background model. Using the metrics of recall, precision and ARI (Adjusted Rand Index), [Formula: see text] improves the binning performance in 28 out of 30 testing experiments (6 datasets with 5 binning tools). The [Formula: see text] is available at https://github.com/kunWangkun/d2SBin .
Experiments showed that [Formula: see text] accurately measures the dissimilarity between contigs of metagenomic reads and that relative sequence composition is more reasonable to bin the contigs. The [Formula: see text] can be applied to any existing contig-binning tools for single metagenomic samples to obtain better binning results.

BMC bioinformatics, 2017-09, Vol.18 (1), p.425-425

Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity

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Improving contig binning of metagenomic data using d 2 S $$ {d}_2^S $$ oligonucleotide frequency dissimilarity

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Improving contig binning of metagenomic data using d2S\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage...

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Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity

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