Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

M Chiara, AM D'Erchia, C Gissi… - Briefings in …, 2021 - academic.oup.com
Various next generation sequencing (NGS) based strategies have been successfully used in
the recent past for tracing origins and understanding the evolution of infectious agents …

[HTML][HTML] Long walk to genomics: History and current approaches to genome sequencing and assembly

AM Giani, GR Gallo, L Gianfranceschi… - Computational and …, 2020 - Elsevier
Genomes represent the starting point of genetic studies. Since the discovery of DNA
structure, scientists have devoted great efforts to determine their sequence in an exact way …

[HTML][HTML] Twelve quick steps for genome assembly and annotation in the classroom

H Jung, T Ventura, JS Chung, WJ Kim… - PLoS computational …, 2020 - journals.plos.org
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-
funded international consortia, have become increasingly affordable, thus fitting the budgets …

Molluscan genomics: the road so far and the way forward

A Gomes-dos-Santos, M Lopes-Lima, LFC Castro… - Hydrobiologia, 2020 - Springer
Mollusca is the second most species-rich phylum within the metazoans, displaying critical
economic, ecological and scientific importance. Yet, they are still largely underrepresented …

Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial …

X Zhang, H Chen, Y Ni, B Wu, J Li… - Molecular Ecology …, 2024 - Wiley Online Library
Tools for visualizing genomes are essential for investigating genomic features and their
interactions. Currently, tools designed originally for animal mitogenomes and plant …

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

A Whibley, JL Kelley, SR Narum - 2021 - Wiley Online Library
The quality of genome assemblies has improved rapidly in recent years due to continual
advances in sequencing technology, assembly approaches, and quality control. In the field …

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

CJ Norsigian, X Fang, Y Seif, JM Monk, BO Palsson - Nature protocols, 2020 - nature.com
Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and
used over the past 20 years. Recently, with the number of genome sequences exponentially …

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

TN Generalovic, SA McCarthy, IA Warren, JMD Wood… - G3, 2021 - academic.oup.com
Abstract Hermetia illucens L.(Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an
increasingly important species for bioconversion of organic material into animal feed. We …

bitacora: A comprehensive tool for the identification and annotation of gene families in genome assemblies

J Vizueta, A Sánchez‐Gracia, J Rozas - 2020 - Wiley Online Library
Gene annotation is a critical bottleneck in genomic research, especially for the
comprehensive study of very large gene families in the genomes of nonmodel organisms …

[HTML][HTML] First draft genome assembly of the desert locust, Schistocerca gregaria

H Verlinden, L Sterck, J Li, Z Li, A Yssel… - …, 2020 - ncbi.nlm.nih.gov
Background: At the time of publication, the most devastating desert locust crisis in decades
is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is …