BackgroundThere is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.FindingsTo overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.ConclusionsBenchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Abstract. The mixing layer is an important meteorological factor that affects air pollution. In this study, the atmospheric mixing layer height (MLH) was observed in Beijing from July 2009 to December 2012 using a ceilometer. By comparison with radiosonde data, we found that the ceilometer underestimates the MLH under conditions of neutral stratification caused by strong winds, whereas it overestimates the MLH when sand-dust is crossing. Using meteorological, PM2.5, and PM10 observational data, we screened the observed MLH automatically; the ceilometer observations were fairly consistent with the radiosondes, with a correlation coefficient greater than 0.9. Further analysis indicated that the MLH is low in autumn and winter and high in spring and summer in Beijing. There is a significant correlation between the sensible heat flux and MLH, and the diurnal cycle of the MLH in summer is also affected by the circulation of mountainous plain winds. Using visibility as an index to classify the degree of air pollution, we found that the variation in the sensible heat and buoyancy term in turbulent kinetic energy (TKE) is insignificant when visibility decreases from 10 to 5 km, but the reduction of shear term in TKE is near 70 %. When visibility decreases from 5 to 1 km, the variation of the shear term in TKE is insignificant, but the decrease in the sensible heat and buoyancy term in TKE is approximately 60 %. Although the correlation between the daily variation of the MLH and visibility is very poor, the correlation between them is significantly enhanced when the relative humidity increases beyond 80 %. This indicates that humidity-related physicochemical processes is the primary source of atmospheric particles under heavy pollution and that the dissipation of atmospheric particles mainly depends on the MLH. The presented results of the atmospheric mixing layer provide useful empirical information for improving meteorological and atmospheric chemistry models and the forecasting and warning of air pollution.

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