BackgroundNext generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy.ResultsSequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform.ConclusionsAll three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.

The simultaneous sequencing of a single cell's genome and transcriptome offers a powerful means to dissect genetic variation and its effect on gene expression. Here we describe G&T-seq, a method for separating and sequencing genomic DNA and full-length mRNA from single cells. By applying G&T-seq to over 220 single cells from mice and humans, we discovered cellular properties that could not be inferred from DNA or RNA sequencing alone.

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Rational design of geosynthetic-reinforced, column-supported embankments requires realistic estimates of the portion of the embankment load that acts vertically downward on the geosynthetic in the area underlain by the foundation soil located between columns. This vertical load can then be used to calculate the strain and tension that develops in the plane of the geosynthetic reinforcement. Several simplified methods are available for calculating the vertical load acting on the geosynthetic, but these methods produce dramatically different results, and there is not agreement regarding which method produces the best estimates. Axisymmetric numerical modeling provides an alternative approach for determining the vertical stresses that develop in the embankment and act on the geosynthetic reinforcement. In this research, axisymmetric numerical modeling is verified against: (1) instrumentation data from a full-scale column-supported test embankment, albeit without geosynthetic reinforcement, at the I-95/Route 1 Interchange project in Virginia, USA; (2) an analytic solution for a disk of membrane material that is pinned at its outer edge and subject to a vertical stress; (3) instrumentation data from a pilot-scale test of a geosynthetic-reinforced, column-supported embankment conducted at the University of Kassel in Germany; and (4) three-dimensional numerical analyses. The results demonstrate that drained axisymmetric numerical analyses using a mesh of linear elastic zones to represent the geosynthetic reinforcement produce results in good agreement with instrumentation data, the analytic solution, and three-dimensional analyses.

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