Environmental resistome risks of wastewaters and aquatic environments deciphered by shotgun metagenomic assembly.
Sign Up to like & getrecommendations! Published in 2020 at "Ecotoxicology and environmental safety"
DOI: 10.1016/j.ecoenv.2020.110612
Abstract: In this paper, we deciphered the core resistome disseminating from hospital wastewater to the aquatic environment by characterising the resistome, plasmidome, mobilome and virulome using metagenomic analysis. This study also elucidated different environmental resistome risks… read more here.
Keywords: environmental resistome; resistome risks; shotgun metagenomic; wastewater ... See more keywords
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad050
Abstract: Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated… read more here.
Keywords: short read; metagenomic assembly; accuracy; resistance genes ... See more keywords
Generation and application of pseudo–long reads for metagenome assembly
Sign Up to like & getrecommendations! Published in 2022 at "GigaScience"
DOI: 10.1093/gigascience/giac044
Abstract: Abstract Background Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and… read more here.
Keywords: long reads; pseudo long; metagenomic assembly; short reads ... See more keywords
Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research
Sign Up to like & getrecommendations! Published in 2022 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.04282-22
Abstract: Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to… read more here.
Keywords: assembly binning; metagenomic assembly; duplicate reads; coverage ... See more keywords