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 …

The Human Pangenome Project: a global resource to map genomic diversity

T Wang, L Antonacci-Fulton, K Howe, HA Lawson… - Nature, 2022‏ - nature.com
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 …

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 …

The design and construction of reference pangenome graphs with minigraph

H Li, X Feng, C Chu - Genome biology, 2020‏ - Springer
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 …

[HTML][HTML] Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

KL Wyres, KE Holt - Current opinion in microbiology, 2018‏ - Elsevier
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 …

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 …

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 …

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 …

Roary: rapid large-scale prokaryote pan genome analysis

AJ Page, CA Cummins, M Hunt, VK Wong… - …, 2015‏ - academic.oup.com
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 …

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 …