Strain-level epidemiology of microbial communities and the human microbiome

Y Yan, LH Nguyen, EA Franzosa, C Huttenhower - Genome medicine, 2020 - Springer
The biological importance and varied metabolic capabilities of specific microbial strains
have long been established in the scientific community. Strains have, in the past, been …

[HTML][HTML] Advances in genomics and genome editing for breeding next generation of fruit and nut crops

S Savadi, S Mangalassery, MS Sandesh - Genomics, 2021 - Elsevier
Fruit tree crops are an essential part of the food production systems and are key to achieve
food and nutrition security. Genetic improvement of fruit trees by conventional breeding has …

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

A Rai, H Hirakawa, R Nakabayashi, S Kikuchi… - Nature …, 2021 - nature.com
Plant genomes remain highly fragmented and are often characterized by hundreds to
thousands of assembly gaps. Here, we report chromosome-level reference and phased …

De novo assembly of a new Olea europaea genome accession using nanopore sequencing

G Rao, J Zhang, X Liu, C Lin, H Xin, L Xue… - Horticulture …, 2021 - academic.oup.com
Olive (Olea europaea L.) is internationally renowned for its high-end product, extra virgin
olive oil. An incomplete genome of O. europaea was previously obtained using shotgun …

Comparison of long-read methods for sequencing and assembly of a plant genome

V Murigneux, SK Rai, A Furtado, TJC Bruxner… - …, 2020 - academic.oup.com
Background Sequencing technologies have advanced to the point where it is possible to
generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long …

LRScaf: improving draft genomes using long noisy reads

M Qin, S Wu, A Li, F Zhao, H Feng, L Ding, J Ruan - BMC genomics, 2019 - Springer
Background The advent of third-generation sequencing (TGS) technologies opens the door
to improve genome assembly. Long reads are promising for enhancing the quality of …

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

J Catchen, A Amores, S Bassham - G3: Genes, Genomes …, 2020 - academic.oup.com
The pace of the sequencing and computational assembly of novel reference genomes is
accelerating. Though DNA sequencing technologies and assembly software tools continue …

A comprehensive review of scaffolding methods in genome assembly

J Luo, Y Wei, M Lyu, Z Wu, X Liu, H Luo… - Briefings in …, 2021 - academic.oup.com
In the field of genome assembly, scaffolding methods make it possible to obtain a more
complete and contiguous reference genome, which is the cornerstone of genomic research …

Benchmarking multi-platform sequencing technologies for human genome assembly

J Wang, WP Veldsman, X Fang, Y Huang… - Briefings in …, 2023 - academic.oup.com
Genome assembly is a computational technique that involves piecing together
deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a …

Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies

VH Do, SH Nguyen, DQ Le, TT Nguyen… - Nucleic Acids …, 2024 - academic.oup.com
Whole genome sequencing has increasingly become the essential method for studying the
genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant …