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Complete, closed bacterial genomes from microbiomes using nanopore sequencing - PubMed
Source: pubmed.ncbi.nlm.nih.gov
Article summary:
1. Nanopore sequencing and a workflow called Lathe can be used to assemble closed bacterial genomes from complex microbiomes.
2. This approach was validated with a synthetic mixture of 12 bacterial species, with seven genomes completely assembled into single contigs and three genomes assembled into four or fewer contigs.
3. Nanopore sequencing and assembly improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.
Article analysis:
The article is generally reliable and trustworthy, as it provides evidence for its claims through the use of a synthetic mixture of 12 bacterial species to validate the approach, as well as analysis of metagenomics data from 13 human stool samples. The authors also declare no competing interests, which further adds to the trustworthiness of the article. However, there are some potential biases that should be noted. For example, the authors do not explore any counterarguments or alternative approaches to nanopore sequencing and assembly that could potentially yield better results than their proposed method. Additionally, they do not discuss any possible risks associated with using nanopore sequencing and assembly for this purpose, such as potential errors in the data due to low nucleotide accuracy compared with alternative sequencing and assembly approaches. Furthermore, they do not present both sides equally when discussing the advantages of their approach over short-read assembly; while they note that their approach improves assembly contiguity, they do not mention any potential drawbacks or limitations that may arise from using nanopore sequencing instead of short-read sequencing.