Background: Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.Results: Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). Conclusions:HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito's largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.

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As our title implies, we consider materials failure at the fundamental level of atomic bond breaking and motion. Using computational molecular dynamics, scalable parallel computers and visualization, we are studying the failure of notched solids under tension using in excess of 10 8 atoms. In rapid brittle fracture, two of the most intriguing features are the roughening of a crack's surface with increasing speed and the terminal crack speed which is much less than the theoretical prediction. Our two-dimensional simulations show conclusively that a dynamic instability of the crack motion occurs as it approaches one-third of the surface sound speed. This discovery provides an explanation for the crack's surface roughening and limiting speed. For three-dimensional slabs, we find that an intrinsically ductile FCC crystal can experience brittle failure for certain crack orientations. A dynamic instability also occurs, but brittle failure is not maintained. The instability is immediately followed by a brittle-to-ductile transition and plasticity. Hyperelasticity, or the elasticity near failure, governs many of the failure processes observed in our simulations and its many roles are elucidated. 'Refrain from immediately resorting to a jackhammer to break open a hazelnut without first checking for an incipient crack on the surface of the shell.' P-G de Gennes ¶ 'You may think I have used a hammer to crack eggs, but I have cracked eggs.' S Chandrasekhar + * Based on Plenary Talk given at PC'97 by FFA.