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Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods
Related publications (32)
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Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...
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Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...
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EPFL2024Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium
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Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...
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Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...
WILEY2022Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics
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2022Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR
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Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained fro ...
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Tamar Kohn, Xavier Fernandez Cassi, Federica Cariti, Alex Tunas Corzon, Timothy R. Julian, Carola Bänziger
The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating vi ...
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Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...
2020A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads
Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficien ...
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