ART: a next-generation sequencing read simulator

Huang, Weichun; Li, Leping; Myers, Jason R.; Marth, Gábor

doi:10.1093/bioinformatics/btr708

Cited by 1,379 publications

(1,313 citation statements)

References 8 publications

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“…To investigate the extent of this issue, we performed read simulation studies (Huang et al 2012) which showed that most paralogs are accurately mappable, and we excluded from further analysis those genes that are not mappable (see Supplemental Methods; Supplemental Fig. S7).…”

Section: Evolution Of H3k27me3 Is More Rapid In Gene Duplicatesmentioning

confidence: 99%

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

Arthur

Slattery

et al. 2014

Genome Res.

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Histone modifications are critical for the regulation of gene expression, cell type specification, and differentiation. However, evolutionary patterns of key modifications that regulate gene expression in differentiating organisms have not been examined. Here we mapped the genomic locations of the repressive mark histone 3 lysine 27 trimethylation (H3K27me3) in four species of Drosophila, and compared these patterns to those in C. elegans. We found that patterns of H3K27me3 are highly conserved across species, but conservation is substantially weaker among duplicated genes. We further discovered that retropositions are associated with greater evolutionary changes in H3K27me3 and gene expression than tandem duplications, indicating that local chromatin constraints influence duplicated gene evolution. These changes are also associated with concomitant evolution of gene expression. Our findings reveal the strong conservation of genomic architecture governed by an epigenetic mark across distantly related species and the importance of gene duplication in generating novel H3K27me3 profiles.[Supplemental material is available for this article.]While transcriptional regulation has long been recognized as a significant target of evolutionary change (King and Wilson 1975), the specific mechanisms behind regulatory divergence have been difficult to dissect (Carroll 2008). In most cases, research has focused on recognizable cis-elements where transcription factors bind in a sequence-specific manner (Borneman et al. 2007;Bradley et al. 2010;Dowell 2010;Ni et al. 2012). Changes to either a transcription factor's DNA-binding properties or transcription factor binding sites (TFBS) enable the evolution of differential regulation, and numerous examples of this phenomenon have been observed (Ludwig et al. 2005;Shultzaberger et al. 2012).Whereas changes in cis-regulatory elements have been implicated in phenotypic and specifically morphological changes (Carroll 2008;Stern and Orgogozo 2008), other components of transcriptional regulation such as the chromatin environment have been scarcely explored (Lenhard et al. 2012). Histone modifications, which are chemical alterations of the histone spools upon which DNA is threaded, constitute one of the best-described elements of chromatin state (Zhou et al. 2011). These modifications can act directly or indirectly (through recruited enzymes) to alter DNA accessibility, thereby controlling other DNA-protein interactions (Campos and Reinberg 2009). Unlike TFBSs, however, histone modifications are not necessarily easily localizable to particular sequence elements, making their evolution difficult to study (Delest et al. 2012).Histone 3 lysine 27 trimethylation (H3K27me3) is one of the best-known histone modifications, in terms of both its biogenesis and effects. H3K27me3 is associated with complex cis-regulatory elements called Polycomb Response Elements (PREs) (Delest et al. 2012). Unlike TFBSs, PREs are compound regulatory elements composed of multiple, sometimes partially redundant, sequen...

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Section: Evolution Of H3k27me3 Is More Rapid In Gene Duplicatesmentioning

confidence: 99%

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

Arthur

Slattery

et al. 2014

Genome Res.

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“…The generated k genomes were saved in a FASTA format file named k-ploid.fa. Second, we used ART (Huang et al, 2012), a next-generation sequencing read simulator, to generate simulated reads from the the k genomes.…”

Section: Results On Simulated Datamentioning

confidence: 99%

H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

et al. 2016

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Motivation: Some economically important plants including wheat and cotton have more than two copies of each chromosome. With the decreasing cost and increasing read length of next-generation sequencing technologies, reconstructing the multiple haplotypes of a polyploid genome from its sequence reads becomes practical. However, the computational challenge in polyploid haplotyping is much greater than that in diploid haplotyping, and there are few related methods. Results: This paper models the polyploid haplotyping problem as an optimal poly-partition problem of the reads, called the Polyploid Balanced Optimal Partition (PBOP) model. For the reads sequenced from a k -ploid genome, the model tries to divide the reads into k groups such that the difference between the reads of the same group is minimized while the difference between the reads of different groups is maximized. When the genotype information is available, the model is extended to the Polyploid Balanced Optimal Partition with Genotype constraint (PBOPG) problem. These models are all NP-hard. We propose two heuristic algorithms, H-PoP and H-PoPG, based on dynamic programming and a strategy of limiting the number of intermediate solutions at each iteration, to solve the two models, respectively. Extensive experimental results on simulated and real data show that our algorithms can solve the models effectively, and are much faster and more accurate than the recent state-of-the-art polyploid haplotyping algorithms. The experiments also show that our algorithms can deal with long reads and deep read coverage effectively and accurately. Furthermore, H-PoP might be applied to help determine the ploidy of an organism. Availability: https://github.com/MinzhuXie/H-PoPG Contact:

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“…To demonstrate that sequence data can be simulated without empirical data in hand, for this case study the sequencing error rate was drawn from the defaults provided with ART. Reads were simulated at an average coverage of 40 reads per site [13].…”

Section: Resultsmentioning

confidence: 99%

“…A user-specified tip will consist of the input anchor genome without any mutations. Using these simulated genomes, TreeToReads calls the read simulation software, ART, [13] to generate Illumina MiSeq paired-end reads. The user can apply a default sequence error model, or use the configuration file to specify an error model generated for observed data.…”

Section: Methodsmentioning

confidence: 99%

TreeToReads - a pipeline for simulating raw reads from phylogenies

McTavish

Pettengill

Davis

et al. 2016

Preprint

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Background: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered. Results: To resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree. Conclusions: Such critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings.

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ART: a next-generation sequencing read simulator

Abstract: Both source and binary software packages are available at http://www.niehs.nih.gov/research/resources/software/art.

Cited by 1,379 publications

References 8 publications

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

TreeToReads - a pipeline for simulating raw reads from phylogenies

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