otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome.
G3 (Bethesda)
; 14(8)2024 Aug 07.
Article
en En
| MEDLINE
| ID: mdl-38861413
ABSTRACT
The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The 2-lined spittlebug, (Prosapia bicincta, Hemiptera Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The 2-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.
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Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Genómica
/
Genoma de los Insectos
Límite:
Animals
Idioma:
En
Revista:
G3 (Bethesda)
Año:
2024
Tipo del documento:
Article
País de afiliación:
Estados Unidos