Metagenomic data assembly–the way of decoding unknown microorganisms

AL Lapidus, AI Korobeynikov - Frontiers in Microbiology, 2021‏ - frontiersin.org
Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …

New approaches for metagenome assembly with short reads

M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020‏ - academic.oup.com
In recent years, the use of longer range read data combined with advances in assembly
algorithms has stimulated big improvements in the contiguity and quality of genome …

Petabase-scale sequence alignment catalyses viral discovery

RC Edgar, B Taylor, V Lin, T Altman, P Barbera… - Nature, 2022‏ - nature.com
Public databases contain a planetary collection of nucleic acid sequences, but their
systematic exploration has been inhibited by a lack of efficient methods for searching this …

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

GL Lin, SB Drysdale, MD Snape, D O'connor… - Nature …, 2024‏ - nature.com
Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory
infection in young children. RSV disease severity is known to be age-dependent and highest …

Genome Detective: an automated system for virus identification from high-throughput sequencing data

M Vilsker, Y Moosa, S Nooij, V Fonseca… - …, 2019‏ - academic.oup.com
Genome Detective is an easy to use web-based software application that assembles the
genomes of viruses quickly and accurately. The application uses a novel alignment method …

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

Y Zheng, S Gao, C Padmanabhan, R Li, M Galvez… - Virology, 2017‏ - Elsevier
Accurate detection of viruses in plants and animals is critical for agriculture production and
human health. Deep sequencing and assembly of virus-derived small interfering RNAs has …

A highly virulent variant of HIV-1 circulating in the Netherlands

C Wymant, D Bezemer, F Blanquart, L Ferretti, A Gall… - Science, 2022‏ - science.org
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred
nine individuals with this variant had a 0.54 to 0.74 log10 increase (ie, a~ 3.5-fold to 5.5-fold …

PHYLOSCANNER: inferring transmission from within-and between-host pathogen genetic diversity

C Wymant, M Hall, O Ratmann, D Bonsall… - Molecular biology …, 2018‏ - academic.oup.com
A central feature of pathogen genomics is that different infectious particles (virions and
bacterial cells) within an infected individual may be genetically distinct, with patterns of …

Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler

SS Shepard, S Meno, J Bahl, MM Wilson, J Barnes… - BMC genomics, 2016‏ - Springer
Background Deep sequencing makes it possible to observe low-frequency viral variants and
sub-populations with greater accuracy and sensitivity than ever before. Existing platforms …

Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013

SJ Watson, P Langat, SM Reid, TTY Lam… - Journal of …, 2015‏ - journals.asm.org
The emergence in humans of the A (H1N1) pdm09 influenza virus, a complex reassortant
virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in …