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 …
sequencing and analysis of combined genomic DNA of entire environmental samples. The …
New approaches for metagenome assembly with short reads
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 …
algorithms has stimulated big improvements in the contiguity and quality of genome …
Petabase-scale sequence alignment catalyses viral discovery
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 …
systematic exploration has been inhibited by a lack of efficient methods for searching this …
Genome Detective: an automated system for virus identification from high-throughput sequencing data
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 …
genomes of viruses quickly and accurately. The application uses a novel alignment method …
A highly virulent variant of HIV-1 circulating in the Netherlands
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 …
nine individuals with this variant had a 0.54 to 0.74 log10 increase (ie, a~ 3.5-fold to 5.5-fold …
VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs
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 …
human health. Deep sequencing and assembly of virus-derived small interfering RNAs has …
Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013
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 …
virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in …
PHYLOSCANNER: inferring transmission from within-and between-host pathogen genetic diversity
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 …
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 …
sub-populations with greater accuracy and sensitivity than ever before. Existing platforms …
Clonal CD4+ T cells in the HIV-1 latent reservoir display a distinct gene profile upon reactivation
Despite suppressive combination antiretroviral therapy (ART), latent HIV-1 proviruses persist
in patients. This latent reservoir is established within 48–72 h after infection, has a long half …
in patients. This latent reservoir is established within 48–72 h after infection, has a long half …