Metagenomics-enabled microbial surveillance
KKK Ko, KR Chng, N Nagarajan - Nature Microbiology, 2022 - nature.com
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential
for zoonoses and emerging infectious diseases that can adversely affect human health …
for zoonoses and emerging infectious diseases that can adversely affect human health …
Genomics in the long-read sequencing era
EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …
explore genomes. While in the early years these methods suffered technical limitations, they …
Oxford Nanopore R10. 4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or …
Abstract Long-read Oxford Nanopore sequencing has democratized microbial genome
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
[HTML][HTML] Expansion of the global RNA virome reveals diverse clades of bacteriophages
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA
virome. Mining 5,150 diverse metatranscriptomes uncovered> 2.5 million RNA virus contigs …
virome. Mining 5,150 diverse metatranscriptomes uncovered> 2.5 million RNA virus contigs …
High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
Metagenome assembly of high-fidelity long reads with hifiasm-meta
De novo assembly of metagenome samples is a common approach to the study of microbial
communities. Current metagenome assemblers developed for short sequence reads or …
communities. Current metagenome assemblers developed for short sequence reads or …
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes
Background The accurate and comprehensive analyses of genome-resolved metagenomics
largely depend on the reconstruction of reference-quality (complete and high-quality) …
largely depend on the reconstruction of reference-quality (complete and high-quality) …
RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes
DH Haft, A Badretdin, G Coulouris… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology
Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million …
Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million …
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially
significant reservoir of microbial biodiversity, yet the majority of desert microorganisms …
significant reservoir of microbial biodiversity, yet the majority of desert microorganisms …
Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement
Assembly of a high-quality genome is important for downstream comparative and functional
genomic studies. However, most tools for genome assembly assessment only give …
genomic studies. However, most tools for genome assembly assessment only give …