Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

DM Bickhart, M Kolmogorov, E Tseng, DM Portik… - Nature …, 2022 - nature.com
Microbial communities might include distinct lineages of closely related organisms that
complicate metagenomic assembly and prevent the generation of complete metagenome …

Beef cattle genome project: Advances in genome sequencing, assembly, and functional genes discovery

Z Gao, Y Lu, Y Chong, M Li, J Hong, J Wu… - International Journal of …, 2024 - mdpi.com
Beef is a major global source of protein, playing an essential role in the human diet. The
worldwide production and consumption of beef continue to rise, reflecting a significant trend …

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

CM Kan, HF Tsang, XM Pei, SSM Ng, AKY Yim… - International Journal of …, 2024 - mdpi.com
Metagenomic sequencing has emerged as a transformative tool in infectious disease
diagnosis, offering a comprehensive and unbiased approach to pathogen detection …

A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces

PJA Skipper, LK Skipper, RA Dixon - Scientific Reports, 2022 - nature.com
There is growing concern surrounding the aesthetic and physical effects of microbial biofilms
on heritage buildings and monuments. Carboniferous stones, such as limestone and …

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

IB Slizovskiy, M Oliva, JK Settle, LV Zyskina, M Prosperi… - Microbiome, 2022 - Springer
Background Metagenomic data can be used to profile high-importance genes within
microbiomes. However, current metagenomic workflows produce data that suffer from low …

Benchmarking genome assembly methods on metagenomic sequencing data

Z Zhang, C Yang, WP Veldsman, X Fang… - Briefings in …, 2023 - academic.oup.com
Metagenome assembly is an efficient approach to reconstruct microbial genomes from
metagenomic sequencing data. Although short-read sequencing has been widely used for …

ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

X Liang, J Zhang, Y Kim, J Ho, K Liu, I Keenum… - Frontiers in …, 2023 - frontiersin.org
Antibiotic resistance is of crucial interest to both human and animal medicine. It has been
recognized that increased environmental monitoring of antibiotic resistance is needed …

The Bioinformatic Applications of Hi-C and Linked Reads

L Jiang, MA Quail, J Fraser-Govil… - Genomics …, 2024 - academic.oup.com
Long-range sequencing grants insight into additional genetic information beyond what can
be accessed by both short reads and modern long-read technology. Several new …

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing

DM Bickhart, M Kolmogorov, E Tseng, DM Portik… - bioRxiv, 2021 - biorxiv.org
Microbial communities in many environments include distinct lineages of closely related
organisms which have proved challenging to separate in metagenomic assembly …

Exploring high-quality microbial genomes by assembly of linked-reads with high barcode specificity using deep learning

Z Zhang, H Wang, C Yang, Y Huang, Z Yue, Y Chen… - bioRxiv, 2022 - biorxiv.org
De novo assembly of metagenomic sequencing data plays an essential role in elucidating
the genomes of unculturable microbes. Linked-reads, in which short-reads are linked …