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Workshop: Comparative assembly of metagenomic sequences
2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2012Next-generation sequencing technologies permit metagenomic studies to characterize the entire bacterial community within an environment by producing a large amount of short noisy DNA reads. One of the most challenging computational tasks is to assemble millions of short reads into longer contigs, which are used as the basis of subsequent computational ...
Bo Liu 0021, Mihai Pop
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Metagenome Assembly and Functional Annotation
2017This chapter reviews metagenome de novo assembly and currently available assembly algorithms and tools. Challenges and opportunities from metagenomic assembly are presented, with a summary of a typical metagenomic assembly workflow. Finally, approaches to reduce large datasets and identify the functions of assembled genes are also discussed.
Adina Howe, Fan Yang, Qingpeng Zhang
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Metagenome-assembled genomes: concepts, analogies, and challenges
Biophysical Reviews, 2021Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenome data. In the last few years, many thousands of MAGs have been reported in the literature, for a variety of environments and host-associated microbiota, including humans.
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Parallel and Memory-Efficient Preprocessing for Metagenome Assembly
2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2017The analysis of high-throughput metagenomic sequencingdata poses significant computational challenges. Mostcurrent de novo assembly tools use the de Bruijn graph-basedmethodology. In prior work, a connected components decompositionof the de Bruijn graph and subsequent partitioningof sequence read data was shown to be an effective memory ...
Vasudevan Rengasamy +2 more
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An Improved Method for Assembling Metagenomic Sequences
2023 International Conference on System Science and Engineering (ICSSE), 2023Nguyen Phi Khanh, Le Van Vinh
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Reference-guided assembly of metagenomes
2020Microorganisms play an important role in all of the Earth's ecosystems, and are critical for the health of humans [1], plants, and animals. Most microbes are not easily cultured [2]; yet, Metagenomics, the analysis of organismal DNA sequences obtained directly from an environmental sample, enables the study of these microorganisms. Metagenomic assembly
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How to Obtain and Compare Metagenome-Assembled Genomes
Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation ...Fabio Beltrame Sanchez +2 more
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Metagenome assembly through clustering of next-generation sequencing data using protein sequences
Journal of Microbiological Methods, 2015Jaebum Kim
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