Fuzzy indication of reliability in metagenomics NGS data analysis
نویسندگان
چکیده
NGS data processing in metagenomics studies has to deal with noisy data that can contain a large amount of reading errors which are difficult to detect and account for. This work introduces a fuzzy indicator of reliability technique to facilitate solutions to this problem. It includes modified Hamming and Levenshtein distance functions that are aimed to be used as drop-in replacements in NGS analysis procedures which rely on distances, such as phylogenetic tree construction. The distances utilise fuzzy sets of reliable bases or an equivalent fuzzy logic, potentially aggregating multiple sources of base reliability.
منابع مشابه
An Introduction to the Use of Fuzzy Mathematics in Archeology (Case Study: Virtual Reconstruction of Togrul Tower by Using Fuzzy Reliability)
Nowadays, the use of fuzzy mathematics and fuzzy logic are increasing in various sciences. Archaeology is one of the sciences that is less attended with the methods of fuzzy mathematics and fuzzy logic. Due to the nature of many archaeological data, however, the use of such methods in archaeology can be beneficial. In this research, it has been tried to explain applications of fuzzy logic and f...
متن کاملTropical Soil Metagenome Library Reveals Complex Microbial Assemblage
2 In this work, we characterized the metagenome of a Malaysian mangrove soil sample via next 3 generation sequencing (NGS). Shotgun NGS data analysis revealed high diversity of microbes 4 from Bacteria and Archaea domains. The metabolic potential of the metagenome was 5 reconstructed using the NGS data and the SEED classification in MEGAN shows abundance of 6 virulence factor genes, implying th...
متن کاملAN AGGREGATED FUZZY RELIABILITY INDEX FOR SLOPE STABILITY ANALYSIS
While sophisticated analytical methods like Morgenstern-Price or finite elementmethods are available for more realistic analysis of stability of slopes, assessment of the exactvalues of soil parameters is practically impossible. Uncertainty in the soil parameters arisesfrom two different sources: scatter in data and systematic error inherent in the estimate of soilproperties. Hence, stability o...
متن کاملAlignment-Free Sequence Analysis and Applications
Genome and metagenome comparisons based on large amounts of next generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they ...
متن کاملMetagenomics study of endophytic bacteria in Aloe vera using next-generation technology
Next generation sequencing (NGS) enables rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of endophytic bacteria in Aloe vera plant, by assessing its PCR amplicon of 16S rDNA sequences (V3-V4 regions) with the Illumina metagenomics technique used to generate a total of 5,199,1...
متن کامل