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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 …
The Human Pangenome Project: a global resource to map genomic diversity
The human reference genome is the most widely used resource in human genetics and is
due for a major update. Its current structure is a linear composite of merged haplotypes from …
due for a major update. Its current structure is a linear composite of merged haplotypes from …
Genomic variation in 3,010 diverse accessions of Asian cultivated rice
W Wang, R Mauleon, Z Hu, D Chebotarov, S Tai, Z Wu… - Nature, 2018 - nature.com
Here we analyse genetic variation, population structure and diversity among 3,010 diverse
Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our …
Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our …
The design and construction of reference pangenome graphs with minigraph
The recent advances in sequencing technologies enable the assembly of individual
genomes to the quality of the reference genome. How to integrate multiple genomes from …
genomes to the quality of the reference genome. How to integrate multiple genomes from …
[HTML][HTML] Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria
Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency
and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant …
and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant …
Pangenome graphs
JM Eizenga, AM Novak, JA Sibbesen… - Annual review of …, 2020 - annualreviews.org
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
A review of methods and databases for metagenomic classification and assembly
FP Breitwieser, J Lu, SL Salzberg - Briefings in bioinformatics, 2019 - academic.oup.com
Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …
methods that seek to make sense of large, complex data sets. Here, we survey two of the …
Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
S Argimón, K Abudahab, RJE Goater… - Microbial …, 2016 - microbiologyresearch.org
Visualization is frequently used to aid our interpretation of complex datasets. Within
microbial genomics, visualizing the relationships between multiple genomes as a tree …
microbial genomics, visualizing the relationships between multiple genomes as a tree …
Roary: rapid large-scale prokaryote pan genome analysis
A typical prokaryote population sequencing study can now consist of hundreds or thousands
of isolates. Interrogating these datasets can provide detailed insights into the genetic …
of isolates. Interrogating these datasets can provide detailed insights into the genetic …
BPGA-an ultra-fast pan-genome analysis pipeline
NM Chaudhari, VK Gupta, C Dutta - Scientific reports, 2016 - nature.com
Recent advances in ultra-high-throughput sequencing technology and metagenomics have
led to a paradigm shift in microbial genomics from few genome comparisons to large-scale …
led to a paradigm shift in microbial genomics from few genome comparisons to large-scale …