An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

Summary: Bisulfite sequencing allows cytosine methylation, an important epigenetic marker, to be detected via nucleotide substitutions. Since the Applied Biosystems SOLiD System uses a unique di-base encoding that increases confidence in the detection of nucleotide substitutions, it is a potentially advantageous platform for this application. However, the di-base encoding also makes reads with many nucleotide substitutions difficult to align to a reference sequence with existing tools, preventing the platform's potential utility for bisulfite sequencing from being realized. Here, we present SOCS-B, a reference-based, un-gapped alignment algorithm for the SOLiD System that is tolerant of both bisulfite-induced nucleotide substitutions and a parametric number of sequencing errors, facilitating bisulfite sequencing on this platform. An implementation of the algorithm has been integrated with the previously reported SOCS alignment tool, and was used to align CpG methylation-enriched Arabidopsis thaliana bisulfite sequence data, exhibiting a 2-fold increase in sensitivity compared to existing methods for aligning SOLiD bisulfite data

Revealing Perceptual Proxies in Comparative Data Visualization

Data Visualization has long been shaped by empirical evidence of the efficacies of different encodings, such as length, position, or area, in conveying quantities. Less is known, however, about what may affect comparison of multiple data series, which generally involves extraction of higher-order values, such as means, ranges, and correlations. In this work, we investigate such factors and the underlying visual processes that may account for them. We begin with a case study motivating the research, in which we modify Krona, a Bioinformatics visualization system, to support several types of comparison. Next, we empirically examine the influence of “arrangement”—that is, whether charts are shown side-by-side, stacked vertically, overlaid, etc.—on comparative tasks, in a series of psychophysical experiments. The results suggest a complex interaction of factors, with different comparative arrangements providing benefits for different combinations of tasks and encodings. For example, overlaid charts make detecting differences easier but comparing means or ranges more difficult. While these results offer some guidance to designers, the number of interactions makes it infeasible to provide broad rankings of arrangements, as has been done previously for encodings. Our subsequent efforts thus work toward understanding the visual processes that underlie the extraction of statistical summaries needed for comparison. It has recently been proposed that simpler shortcuts, called Perceptual Proxies, are used by the visual system to estimate these values. We investigate proxies for bar charts in experiments using an “adversarial” framework, in which the ranking of two charts along a task metric (e.g. mean) is opposite their ranking along a proxy metric (e.g. convex hull area). The strongest evidence we find is for use of a “centroid” proxy to estimate means in bar charts. Finally, we attempt to use using human-guided optimization to construct charts de novo, without assuming specific proxies. This work contributes both to perceptual psychology, by offering evidence for underlying visual processes that may be involved in the interpretation of comparative visualizations, and to data visualization, by providing new research methods and straightforward design guidance on how best to lay out charts to support certain tasks

Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

MetAMOS: A modular and open source metagenomic assembly and analysis pipeline

© 2013 Treangen et al. We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data

Summary: Bisulfite sequencing, a combination of bisulfite treatment and high-throughput sequencing, has proved to be a valuable method for measuring DNA methylation at single base resolution. Here, we present B-SOLANA, an approach for the analysis of two-base encoding (colorspace) bisulfite sequencing data on the SOLiD platform of Life Technologies. It includes the alignment of bisulfite sequences and the determination of methylation levels in CpG as well as non-CpG sequence contexts. B-SOLANA enables a fast and accurate analysis of large raw sequence datasets

Atmospheric boundary-layer structure observed during a haze event due to forest-fire smoke

During a haze event in Baltimore, U.S.A. from July 6 to 8, 2002, smoke from forest fires in the Québec region (Canada), degraded air quality and impacted upon local climate, decreasing solar radiation and air temperature. The smoke particles in and above the atmospheric boundary layer (ABL) served as a tracer and provided a unique opportunity to investigate the ABL structure, especially entrainment. Elastic backscatter lidar measurements taken during the haze event distinctly reveal the downward sweeps (or wisps) of smoke-laden air from the free atmosphere into the ABL. Visualisations of mechanisms such as dry convection, the entrainment process, detrainment, coherent entrainment structures, and mixing inside the ABL, are presented. Thermals overshooting at the ABL top are shown to create disturbances in the form of gravity waves in the free atmosphere aloft, as evidenced by a corresponding ripple structure at the bottom of the smoke layer. Lidar data, aerosol groundbased measurements and supporting meteorological data are used to link free atmosphere, mixed-layer and ground-level aerosols. During the peak period of the haze event (July 7, 2002), the correlation between time series of elastic backscatter lidar data within the mixed layer and the scattering coefficient from a nephelometer at ground level was found to be high (R ¼ 0.96 for z ¼ 324 m, and R ¼ 0.89 for z ¼ 504 m). Ground-level aerosol concentration was at a maximum about 2 h after the smoke layer intersected with the growing ABL, confirming that the wisps do not initially reach the ground

Aerosol optical characterization by nephelometer and lidar: the Baltimore Supersite experiment during the Canadian forest fire smoke intrusion

[1] High spatial and temporal resolution elastic backscatter lidar data from Baltimore are analyzed with a near-end approach to estimate vertical profiles of the aerosol extinction coefficient. The near-end approach makes use of the (1) aerosol scattering coefficient measured at the surface with a nephelometer (0.530 μm), (2) surface level particle size distribution, and (3) refractive index calculated using Mie theory to estimate the aerosol extinction coefficient boundary condition for the lidar equation. There was a broad range of atmospheric turbidity due to a strong haze event, which occurred because of smoke transport from Canadian forest fires, and led to a wide range of observed atmospheric properties. The index of refraction for aerosols estimated during the entire study period is 1.5–0.47 i, which is typical for soot. The measured surface level aerosol scattering coefficient ranged from σp = 0.002 to σp = 0.541 km−1, and the computed aerosol extinction coefficient spanned values κp = 0.01 to κp = 1.05 km−1. The derived mass concentration and the mass scattering ranges were 3.96–194 μg m−3 and 0.05–3.260 m2g−1, respectively. The aerosol optical properties were dominated by light absorption by soot

Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases,

Previous postmortem microbiome studies have focused on characterizing taxa turnover during an undisturbed decomposition process. How coexisting conditions (e.g., frozen, buried, burned) affect the human microbiome at the time of discovery is less well understood. Microbiome data were collected from two pediatric cases at the Wayne County Medical Examiner in Michigan. The bodies were found frozen, hidden in a freezer for an extended time. Microbial communities were sampled from six external anatomic locations at three time points during the thawing process, prior to autopsy. The 16S rRNA V4 gene amplicon region was sequenced using high‐throughput sequencing (Illumina MiSeq). Microbial diversity increased, and there was a distinct shift in microbial community structure and abundance throughout the thawing process. Overall, these data demonstrate that the postmortem human microbiome changes during the thawing process, and have important forensic implications when bodies have been substantially altered, modified, and concealed after death.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138306/1/jfo13419.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138306/2/jfo13419_am.pd