METHOD: The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization.
RESULTS: Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach.
CONCLUSION: We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
METHODS: This study proposed an end-to-end air quality predictive model for smart city applications, utilizing four machine learning techniques and two deep learning techniques. These include Ada Boost, SVR, RF, KNN, MLP regressor and LSTM. The study was conducted in four different urban cities in Selangor, Malaysia, including Petaling Jaya, Banting, Klang, and Shah Alam. The model considered the air quality data of various pollution markers such as PM2.5, PM10, O3, and CO. Additionally, meteorological data including wind speed and wind direction were also considered, and their interactions with the pollutant markers were quantified. The study aimed to determine the correlation variance of the dependent variable in predicting air pollution and proposed a feature optimization process to reduce dimensionality and remove irrelevant features to enhance the prediction of PM2.5, improving the existing LSTM model. The study estimates the concentration of pollutants in the air based on training and highlights the contribution of feature optimization in air quality predictions through feature dimension reductions.
RESULTS: In this section, the results of predicting the concentration of pollutants (PM2.5, PM10, O3, and CO) in the air are presented in R2 and RMSE. In predicting the PM10 and PM2.5concentration, LSTM performed the best overall high R2values in the four study areas with the R2 values of 0.998, 0.995, 0.918, and 0.993 in Banting, Petaling, Klang and Shah Alam stations, respectively. The study indicated that among the studied pollution markers, PM2.5,PM10, NO2, wind speed and humidity are the most important elements to monitor. By reducing the number of features used in the model the proposed feature optimization process can make the model more interpretable and provide insights into the most critical factor affecting air quality. Findings from this study can aid policymakers in understanding the underlying causes of air pollution and develop more effective smart strategies for reducing pollution levels.