Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Convolution layers are prevalent in many classes of deep neural networks, including Convolutional Neural Networks (CNNs) which provide state-of-the-art results for tasks like image recognition, neural machine translation and speech recognition. The computationally expensive nature of a convolution operation has led to the proliferation of implementations including matrix-matrix multiplication formulation, and direct convolution primarily targeting GPUs. In this paper, we introduce direct convolution kernels for x86 architectures, in particular for Xeon and Xeon Phi systems, which are implemented via a dynamic compilation approach. Our JIT-based implementation shows close to theoretical peak performance, depending on the setting and the CPU architecture at hand. We additionally demonstrate how these JIT-optimized kernels can be integrated into a lightweight multi-node graph execution model. This illustrates that single-and multi-node runs yield high efficiencies and high imagethroughputs when executing state-of-the-art image recognition tasks on CPUs.