Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

McIntyre, Alexa B. R.; Ounit, Rachid; Afshinnekoo, Ebrahim; Prill, Robert J.; Hénaff, Elizabeth; Alexander, Noah; Minot, Sam; Danko, David; Foox, Jonathan; Ahsanuddin, Sofia; Tighe, Scott; Hasan, Nur A.; Subramanian, Poorani; Moffat, Kelly; Levy, Shawn; Lonardi, Stefano; Greenfield, Nick; Colwell, Rita R.; Rosen, Gail; Mason, Christopher E.

doi:10.1101/156919

Cited by 76 publications

(145 citation statements)

References 70 publications

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“…The core intuition behind this approach was that reads from the same fragment would tend to overlap with similar sets of reads that had different barcodes. Though each set of reads with the same barcode can contain reads from several fragments (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20), it is unlikely that two sets of reads with two different barcodes would contain reads from multiple separate overlapping fragments. If multiple reads with the same barcode overlapped with reads that had another barcode it would suggest that the original reads came from the same fragment.…”

Section: Barcode Deconvolution Using a Graphical Modelmentioning

confidence: 99%

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics

Danko

Meleshko

Bezdan

et al. 2017

Preprint

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Emerging linked-read technologies (aka read-cloud or barcoded short-reads) have revived interest in standard short-read technology as a viable way to understand large scale structure in genomes and metagenomes. Linked-read technologies, such as the 10X Chromium system, use a microfluidic system and a set of specially designed 3' barcodes (aka UIDs) to tag short DNA reads which were originally sourced from the same long fragment of DNA; subsequently these specially barcoded reads are sequenced on standard short read platforms. This approach results in interesting compromises. Each long fragment of DNA is covered only sparsely by short reads, no information about the relative ordering of reads from the same fragment is preserved, and typically each 3' barcode matches reads from 5-20 long fragments of DNA. However, the cost per base to sequence is far lower than single molecule long read sequencing systems, far less input DNA is required, and the error rate is that of standard short-reads.Linked-reads represent a new set of algorithmic challenges. In this paper we formally describe one particular issue common to all applications of linked-read technology: the deconvolution of reads with a single barcode into clusters that correspond to a single long fragment of DNA. We introduce Minerva, A graph-based algorithm which approximately solves the barcode deconvolution problem for metagenomic data (where reference genomes may be incomplete or unavailable). Additionally, we demonstrate that deconvolved barcoded reads significantly improve downstream results by improving the specificity of taxonomic assignments, and by improving the ability of topic models to identify clusters of related sequences.

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Section: Barcode Deconvolution Using a Graphical Modelmentioning

confidence: 99%

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics

Danko

Meleshko

Bezdan

et al. 2017

Preprint

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“…All simulated reads in the McIntyre et al [14] study were generated from published complete genomes.…”

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confidence: 99%

“…This dataset is suitable for comparing the completeness of the databases, as well as the sensitivity of the and sensitivity of both tools in addition to six binning tools from [14] are summarized in Figure 2A. As to any species in SILVA [20], which was used as the gold standard in this study.…”

mentioning

confidence: 99%

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

Zhou

Luhmann

Alikhan

et al. 2017

Preprint

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Abstract. Exploring the genetic diversity of microbes within the environment through metagenomic 5 sequencing first requires classifying these reads into taxonomic groups. Current methods compare these 6 sequencing data with existing biased and limited reference databases. Several recent evaluation studies 7 demonstrate that current methods either lack sufficient sensitivity for species-level assignments or suffer 8 from false positives, overestimating the number of species in the metagenome. Both are especially prob-9 lematic for the identification of low-abundance microbial species, e. g. detecting pathogens in ancient 10 metagenomic samples. We present a new method, SPARSE, which improves taxonomic assignments 11 of metagenomic reads. SPARSE balances existing biased reference databases by grouping reference 12 genomes into similarity-based hierarchical clusters, implemented as an efficient incremental data struc-13 ture. SPARSE assigns reads to these clusters using a probabilistic model, which specifically penalizes 14 non-specific mappings of reads from unknown sources and hence reduces false-positive assignments.

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“…We then show that, based 31 on diet content alone, it is possible to pinpoint the sampling location of an individual rat 32 within tens of kilometres. We expect that the rapidly increasing accuracy and 33 throughput of nanopore-based sequencing, as well as increases in the species 34 diversity of genomic databases, will soon allow rapid and unbiased assessments of 35 animal diets in field settings.…”

mentioning

confidence: 99%

“…Page 4 of 34 However, DNA metabarcoding is not free from bias. PCR primers must be specifically 64 tailored to particular sets of taxa or species (Jarman et al 2002).…”

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confidence: 99%

New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

Pearman

Smith

Breckell

et al. 2018

Preprint

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14Introduced species of mammals in New Zealand have had catastrophic effects on 15 populations of diverse native species. Quantifying the diets of these omnivorous and 16 predatory species is critical for understanding which native species are most impacted, 17 and to prioritize which mammal species and locations should be targeted with control 2009). These metabarcoding methods require a PCR step using primers that bind to 24 highly conserved genomic regions (e.g. mitochondrial COI) to amplify specific regions 25 for sequencing. This step introduces significant bias, primarily due to the lack of a 26 universal primer set (King et al. 2008). Here we show that direct metagenomic 27 sequencing using the Oxford Nanopore Minion allows rapid quantification of rat diets. 28Using a sample of rats collected from within 100km of Auckland, NZ, we show that 29 these rats consume a wide variety of plant, invertebrate, vertebrate, and fungal taxa, 30 with substantial differences in diet content between locales. We then show that, based 31 on diet content alone, it is possible to pinpoint the sampling location of an individual rat 32 within tens of kilometres. We expect that the rapidly increasing accuracy and 33 throughput of nanopore-based sequencing, as well as increases in the species 34 diversity of genomic databases, will soon allow rapid and unbiased assessments of 35 animal diets in field settings.

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Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

Cited by 76 publications

References 70 publications

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

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